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-            created at 2024-11-04 14:30 +0000
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&amp;#x27;33499a5b-e3a8-4e42-999a-e027f462b9cc/frame70/dhdl70.xvg&amp;#x27;, &amp;#x27;33499a5b-e3a8-4e42-999a-e027f462b9cc/frame71/dhdl71.xvg&amp;#x27;, &amp;#x27;33499a5b-e3a8-4e42-999a-e027f462b9cc/frame72/dhdl72.xvg&amp;#x27;, &amp;#x27;33499a5b-e3a8-4e42-999a-e027f462b9cc/frame73/dhdl73.xvg&amp;#x27;, &amp;#x27;33499a5b-e3a8-4e42-999a-e027f462b9cc/frame74/dhdl74.xvg&amp;#x27;, &amp;#x27;33499a5b-e3a8-4e42-999a-e027f462b9cc/frame75/dhdl75.xvg&amp;#x27;, &amp;#x27;33499a5b-e3a8-4e42-999a-e027f462b9cc/frame76/dhdl76.xvg&amp;#x27;, &amp;#x27;33499a5b-e3a8-4e42-999a-e027f462b9cc/frame77/dhdl77.xvg&amp;#x27;, &amp;#x27;33499a5b-e3a8-4e42-999a-e027f462b9cc/frame78/dhdl78.xvg&amp;#x27;, &amp;#x27;33499a5b-e3a8-4e42-999a-e027f462b9cc/frame79/dhdl79.xvg&amp;#x27;, &amp;#x27;33499a5b-e3a8-4e42-999a-e027f462b9cc/frame8/dhdl8.xvg&amp;#x27;, &amp;#x27;33499a5b-e3a8-4e42-999a-e027f462b9cc/frame80/dhdl80.xvg&amp;#x27;, &amp;#x27;33499a5b-e3a8-4e42-999a-e027f462b9cc/frame81/dhdl81.xvg&amp;#x27;, &amp;#x27;33499a5b-e3a8-4e42-999a-e027f462b9cc/frame82/dhdl82.xvg&amp;#x27;, &amp;#x27;33499a5b-e3a8-4e42-999a-e027f462b9cc/frame83/dhdl83.xvg&amp;#x27;, &amp;#x27;33499a5b-e3a8-4e42-999a-e027f462b9cc/frame84/dhdl84.xvg&amp;#x27;, &amp;#x27;33499a5b-e3a8-4e42-999a-e027f462b9cc/frame85/dhdl85.xvg&amp;#x27;, &amp;#x27;33499a5b-e3a8-4e42-999a-e027f462b9cc/frame86/dhdl86.xvg&amp;#x27;, &amp;#x27;33499a5b-e3a8-4e42-999a-e027f462b9cc/frame87/dhdl87.xvg&amp;#x27;, &amp;#x27;33499a5b-e3a8-4e42-999a-e027f462b9cc/frame88/dhdl88.xvg&amp;#x27;, &amp;#x27;33499a5b-e3a8-4e42-999a-e027f462b9cc/frame89/dhdl89.xvg&amp;#x27;, &amp;#x27;33499a5b-e3a8-4e42-999a-e027f462b9cc/frame9/dhdl9.xvg&amp;#x27;, &amp;#x27;33499a5b-e3a8-4e42-999a-e027f462b9cc/frame90/dhdl90.xvg&amp;#x27;, &amp;#x27;33499a5b-e3a8-4e42-999a-e027f462b9cc/frame91/dhdl91.xvg&amp;#x27;, &amp;#x27;33499a5b-e3a8-4e42-999a-e027f462b9cc/frame92/dhdl92.xvg&amp;#x27;, &amp;#x27;33499a5b-e3a8-4e42-999a-e027f462b9cc/frame93/dhdl93.xvg&amp;#x27;, &amp;#x27;33499a5b-e3a8-4e42-999a-e027f462b9cc/frame94/dhdl94.xvg&amp;#x27;, &amp;#x27;33499a5b-e3a8-4e42-999a-e027f462b9cc/frame95/dhdl95.xvg&amp;#x27;, &amp;#x27;33499a5b-e3a8-4e42-999a-e027f462b9cc/frame96/dhdl96.xvg&amp;#x27;, &amp;#x27;33499a5b-e3a8-4e42-999a-e027f462b9cc/frame97/dhdl97.xvg&amp;#x27;, &amp;#x27;33499a5b-e3a8-4e42-999a-e027f462b9cc/frame98/dhdl98.xvg&amp;#x27;, &amp;#x27;33499a5b-e3a8-4e42-999a-e027f462b9cc/frame99/dhdl99.xvg&amp;#x27;]\n2024-11-04 14:29:55,959 [MainThread  ] [INFO ]  Extracting: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/xvg_B.zip\n2024-11-04 14:29:55,960 [MainThread  ] [INFO ]  to:\n2024-11-04 14:29:55,960 [MainThread  ] [INFO ]  [&amp;#x27;31c4f888-19a1-49ab-b924-5b903a309a33/frame0/dhdl0.xvg&amp;#x27;, &amp;#x27;31c4f888-19a1-49ab-b924-5b903a309a33/frame1/dhdl1.xvg&amp;#x27;, &amp;#x27;31c4f888-19a1-49ab-b924-5b903a309a33/frame10/dhdl10.xvg&amp;#x27;, &amp;#x27;31c4f888-19a1-49ab-b924-5b903a309a33/frame11/dhdl11.xvg&amp;#x27;, &amp;#x27;31c4f888-19a1-49ab-b924-5b903a309a33/frame12/dhdl12.xvg&amp;#x27;, &amp;#x27;31c4f888-19a1-49ab-b924-5b903a309a33/frame13/dhdl13.xvg&amp;#x27;, &amp;#x27;31c4f888-19a1-49ab-b924-5b903a309a33/frame14/dhdl14.xvg&amp;#x27;, &amp;#x27;31c4f888-19a1-49ab-b924-5b903a309a33/frame15/dhdl15.xvg&amp;#x27;, &amp;#x27;31c4f888-19a1-49ab-b924-5b903a309a33/frame16/dhdl16.xvg&amp;#x27;, &amp;#x27;31c4f888-19a1-49ab-b924-5b903a309a33/frame17/dhdl17.xvg&amp;#x27;, &amp;#x27;31c4f888-19a1-49ab-b924-5b903a309a33/frame18/dhdl18.xvg&amp;#x27;, &amp;#x27;31c4f888-19a1-49ab-b924-5b903a309a33/frame19/dhdl19.xvg&amp;#x27;, &amp;#x27;31c4f888-19a1-49ab-b924-5b903a309a33/frame2/dhdl2.xvg&amp;#x27;, &amp;#x27;31c4f888-19a1-49ab-b924-5b903a309a33/frame20/dhdl20.xvg&amp;#x27;, &amp;#x27;31c4f888-19a1-49ab-b924-5b903a309a33/frame21/dhdl21.xvg&amp;#x27;, &amp;#x27;31c4f888-19a1-49ab-b924-5b903a309a33/frame22/dhdl22.xvg&amp;#x27;, &amp;#x27;31c4f888-19a1-49ab-b924-5b903a309a33/frame23/dhdl23.xvg&amp;#x27;, &amp;#x27;31c4f888-19a1-49ab-b924-5b903a309a33/frame24/dhdl24.xvg&amp;#x27;, &amp;#x27;31c4f888-19a1-49ab-b924-5b903a309a33/frame25/dhdl25.xvg&amp;#x27;, &amp;#x27;31c4f888-19a1-49ab-b924-5b903a309a33/frame26/dhdl26.xvg&amp;#x27;, &amp;#x27;31c4f888-19a1-49ab-b924-5b903a309a33/frame27/dhdl27.xvg&amp;#x27;, &amp;#x27;31c4f888-19a1-49ab-b924-5b903a309a33/frame28/dhdl28.xvg&amp;#x27;, &amp;#x27;31c4f888-19a1-49ab-b924-5b903a309a33/frame29/dhdl29.xvg&amp;#x27;, &amp;#x27;31c4f888-19a1-49ab-b924-5b903a309a33/frame3/dhdl3.xvg&amp;#x27;, &amp;#x27;31c4f888-19a1-49ab-b924-5b903a309a33/frame30/dhdl30.xvg&amp;#x27;, &amp;#x27;31c4f888-19a1-49ab-b924-5b903a309a33/frame31/dhdl31.xvg&amp;#x27;, &amp;#x27;31c4f888-19a1-49ab-b924-5b903a309a33/frame32/dhdl32.xvg&amp;#x27;, &amp;#x27;31c4f888-19a1-49ab-b924-5b903a309a33/frame33/dhdl33.xvg&amp;#x27;, &amp;#x27;31c4f888-19a1-49ab-b924-5b903a309a33/frame34/dhdl34.xvg&amp;#x27;, &amp;#x27;31c4f888-19a1-49ab-b924-5b903a309a33/frame35/dhdl35.xvg&amp;#x27;, &amp;#x27;31c4f888-19a1-49ab-b924-5b903a309a33/frame36/dhdl36.xvg&amp;#x27;, &amp;#x27;31c4f888-19a1-49ab-b924-5b903a309a33/frame37/dhdl37.xvg&amp;#x27;, &amp;#x27;31c4f888-19a1-49ab-b924-5b903a309a33/frame38/dhdl38.xvg&amp;#x27;, &amp;#x27;31c4f888-19a1-49ab-b924-5b903a309a33/frame39/dhdl39.xvg&amp;#x27;, &amp;#x27;31c4f888-19a1-49ab-b924-5b903a309a33/frame4/dhdl4.xvg&amp;#x27;, &amp;#x27;31c4f888-19a1-49ab-b924-5b903a309a33/frame40/dhdl40.xvg&amp;#x27;, &amp;#x27;31c4f888-19a1-49ab-b924-5b903a309a33/frame41/dhdl41.xvg&amp;#x27;, &amp;#x27;31c4f888-19a1-49ab-b924-5b903a309a33/frame42/dhdl42.xvg&amp;#x27;, &amp;#x27;31c4f888-19a1-49ab-b924-5b903a309a33/frame43/dhdl43.xvg&amp;#x27;, &amp;#x27;31c4f888-19a1-49ab-b924-5b903a309a33/frame44/dhdl44.xvg&amp;#x27;, &amp;#x27;31c4f888-19a1-49ab-b924-5b903a309a33/frame45/dhdl45.xvg&amp;#x27;, &amp;#x27;31c4f888-19a1-49ab-b924-5b903a309a33/frame46/dhdl46.xvg&amp;#x27;, &amp;#x27;31c4f888-19a1-49ab-b924-5b903a309a33/frame47/dhdl47.xvg&amp;#x27;, &amp;#x27;31c4f888-19a1-49ab-b924-5b903a309a33/frame48/dhdl48.xvg&amp;#x27;, &amp;#x27;31c4f888-19a1-49ab-b924-5b903a309a33/frame49/dhdl49.xvg&amp;#x27;, &amp;#x27;31c4f888-19a1-49ab-b924-5b903a309a33/frame5/dhdl5.xvg&amp;#x27;, &amp;#x27;31c4f888-19a1-49ab-b924-5b903a309a33/frame50/dhdl50.xvg&amp;#x27;, &amp;#x27;31c4f888-19a1-49ab-b924-5b903a309a33/frame51/dhdl51.xvg&amp;#x27;, &amp;#x27;31c4f888-19a1-49ab-b924-5b903a309a33/frame52/dhdl52.xvg&amp;#x27;, &amp;#x27;31c4f888-19a1-49ab-b924-5b903a309a33/frame53/dhdl53.xvg&amp;#x27;, &amp;#x27;31c4f888-19a1-49ab-b924-5b903a309a33/frame54/dhdl54.xvg&amp;#x27;, &amp;#x27;31c4f888-19a1-49ab-b924-5b903a309a33/frame55/dhdl55.xvg&amp;#x27;, &amp;#x27;31c4f888-19a1-49ab-b924-5b903a309a33/frame56/dhdl56.xvg&amp;#x27;, &amp;#x27;31c4f888-19a1-49ab-b924-5b903a309a33/frame57/dhdl57.xvg&amp;#x27;, &amp;#x27;31c4f888-19a1-49ab-b924-5b903a309a33/frame58/dhdl58.xvg&amp;#x27;, &amp;#x27;31c4f888-19a1-49ab-b924-5b903a309a33/frame59/dhdl59.xvg&amp;#x27;, &amp;#x27;31c4f888-19a1-49ab-b924-5b903a309a33/frame6/dhdl6.xvg&amp;#x27;, &amp;#x27;31c4f888-19a1-49ab-b924-5b903a309a33/frame60/dhdl60.xvg&amp;#x27;, &amp;#x27;31c4f888-19a1-49ab-b924-5b903a309a33/frame61/dhdl61.xvg&amp;#x27;, &amp;#x27;31c4f888-19a1-49ab-b924-5b903a309a33/frame62/dhdl62.xvg&amp;#x27;, &amp;#x27;31c4f888-19a1-49ab-b924-5b903a309a33/frame63/dhdl63.xvg&amp;#x27;, &amp;#x27;31c4f888-19a1-49ab-b924-5b903a309a33/frame64/dhdl64.xvg&amp;#x27;, &amp;#x27;31c4f888-19a1-49ab-b924-5b903a309a33/frame65/dhdl65.xvg&amp;#x27;, &amp;#x27;31c4f888-19a1-49ab-b924-5b903a309a33/frame66/dhdl66.xvg&amp;#x27;, &amp;#x27;31c4f888-19a1-49ab-b924-5b903a309a33/frame67/dhdl67.xvg&amp;#x27;, &amp;#x27;31c4f888-19a1-49ab-b924-5b903a309a33/frame68/dhdl68.xvg&amp;#x27;, &amp;#x27;31c4f888-19a1-49ab-b924-5b903a309a33/frame69/dhdl69.xvg&amp;#x27;, &amp;#x27;31c4f888-19a1-49ab-b924-5b903a309a33/frame7/dhdl7.xvg&amp;#x27;, &amp;#x27;31c4f888-19a1-49ab-b924-5b903a309a33/frame70/dhdl70.xvg&amp;#x27;, &amp;#x27;31c4f888-19a1-49ab-b924-5b903a309a33/frame71/dhdl71.xvg&amp;#x27;, &amp;#x27;31c4f888-19a1-49ab-b924-5b903a309a33/frame72/dhdl72.xvg&amp;#x27;, &amp;#x27;31c4f888-19a1-49ab-b924-5b903a309a33/frame73/dhdl73.xvg&amp;#x27;, &amp;#x27;31c4f888-19a1-49ab-b924-5b903a309a33/frame74/dhdl74.xvg&amp;#x27;, &amp;#x27;31c4f888-19a1-49ab-b924-5b903a309a33/frame75/dhdl75.xvg&amp;#x27;, &amp;#x27;31c4f888-19a1-49ab-b924-5b903a309a33/frame76/dhdl76.xvg&amp;#x27;, &amp;#x27;31c4f888-19a1-49ab-b924-5b903a309a33/frame77/dhdl77.xvg&amp;#x27;, &amp;#x27;31c4f888-19a1-49ab-b924-5b903a309a33/frame78/dhdl78.xvg&amp;#x27;, &amp;#x27;31c4f888-19a1-49ab-b924-5b903a309a33/frame79/dhdl79.xvg&amp;#x27;, &amp;#x27;31c4f888-19a1-49ab-b924-5b903a309a33/frame8/dhdl8.xvg&amp;#x27;, &amp;#x27;31c4f888-19a1-49ab-b924-5b903a309a33/frame80/dhdl80.xvg&amp;#x27;, &amp;#x27;31c4f888-19a1-49ab-b924-5b903a309a33/frame81/dhdl81.xvg&amp;#x27;, &amp;#x27;31c4f888-19a1-49ab-b924-5b903a309a33/frame82/dhdl82.xvg&amp;#x27;, &amp;#x27;31c4f888-19a1-49ab-b924-5b903a309a33/frame83/dhdl83.xvg&amp;#x27;, &amp;#x27;31c4f888-19a1-49ab-b924-5b903a309a33/frame84/dhdl84.xvg&amp;#x27;, &amp;#x27;31c4f888-19a1-49ab-b924-5b903a309a33/frame85/dhdl85.xvg&amp;#x27;, &amp;#x27;31c4f888-19a1-49ab-b924-5b903a309a33/frame86/dhdl86.xvg&amp;#x27;, &amp;#x27;31c4f888-19a1-49ab-b924-5b903a309a33/frame87/dhdl87.xvg&amp;#x27;, &amp;#x27;31c4f888-19a1-49ab-b924-5b903a309a33/frame88/dhdl88.xvg&amp;#x27;, &amp;#x27;31c4f888-19a1-49ab-b924-5b903a309a33/frame89/dhdl89.xvg&amp;#x27;, &amp;#x27;31c4f888-19a1-49ab-b924-5b903a309a33/frame9/dhdl9.xvg&amp;#x27;, &amp;#x27;31c4f888-19a1-49ab-b924-5b903a309a33/frame90/dhdl90.xvg&amp;#x27;, &amp;#x27;31c4f888-19a1-49ab-b924-5b903a309a33/frame91/dhdl91.xvg&amp;#x27;, &amp;#x27;31c4f888-19a1-49ab-b924-5b903a309a33/frame92/dhdl92.xvg&amp;#x27;, &amp;#x27;31c4f888-19a1-49ab-b924-5b903a309a33/frame93/dhdl93.xvg&amp;#x27;, &amp;#x27;31c4f888-19a1-49ab-b924-5b903a309a33/frame94/dhdl94.xvg&amp;#x27;, &amp;#x27;31c4f888-19a1-49ab-b924-5b903a309a33/frame95/dhdl95.xvg&amp;#x27;, &amp;#x27;31c4f888-19a1-49ab-b924-5b903a309a33/frame96/dhdl96.xvg&amp;#x27;, &amp;#x27;31c4f888-19a1-49ab-b924-5b903a309a33/frame97/dhdl97.xvg&amp;#x27;, &amp;#x27;31c4f888-19a1-49ab-b924-5b903a309a33/frame98/dhdl98.xvg&amp;#x27;, &amp;#x27;31c4f888-19a1-49ab-b924-5b903a309a33/frame99/dhdl99.xvg&amp;#x27;]\n2024-11-04 14:29:55,962 [MainThread  ] [INFO ]  pmx analyse -fA 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame0/dhdl0.xvg 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame1/dhdl1.xvg 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame10/dhdl10.xvg 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame11/dhdl11.xvg 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame12/dhdl12.xvg 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame13/dhdl13.xvg 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame14/dhdl14.xvg 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame15/dhdl15.xvg 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31c4f888-19a1-49ab-b924-5b903a309a33/frame8/dhdl8.xvg 31c4f888-19a1-49ab-b924-5b903a309a33/frame80/dhdl80.xvg 31c4f888-19a1-49ab-b924-5b903a309a33/frame81/dhdl81.xvg 31c4f888-19a1-49ab-b924-5b903a309a33/frame82/dhdl82.xvg 31c4f888-19a1-49ab-b924-5b903a309a33/frame83/dhdl83.xvg 31c4f888-19a1-49ab-b924-5b903a309a33/frame84/dhdl84.xvg 31c4f888-19a1-49ab-b924-5b903a309a33/frame85/dhdl85.xvg 31c4f888-19a1-49ab-b924-5b903a309a33/frame86/dhdl86.xvg 31c4f888-19a1-49ab-b924-5b903a309a33/frame87/dhdl87.xvg 31c4f888-19a1-49ab-b924-5b903a309a33/frame88/dhdl88.xvg 31c4f888-19a1-49ab-b924-5b903a309a33/frame89/dhdl89.xvg 31c4f888-19a1-49ab-b924-5b903a309a33/frame9/dhdl9.xvg 31c4f888-19a1-49ab-b924-5b903a309a33/frame90/dhdl90.xvg 31c4f888-19a1-49ab-b924-5b903a309a33/frame91/dhdl91.xvg 31c4f888-19a1-49ab-b924-5b903a309a33/frame92/dhdl92.xvg 31c4f888-19a1-49ab-b924-5b903a309a33/frame93/dhdl93.xvg 31c4f888-19a1-49ab-b924-5b903a309a33/frame94/dhdl94.xvg 31c4f888-19a1-49ab-b924-5b903a309a33/frame95/dhdl95.xvg 31c4f888-19a1-49ab-b924-5b903a309a33/frame96/dhdl96.xvg 31c4f888-19a1-49ab-b924-5b903a309a33/frame97/dhdl97.xvg 31c4f888-19a1-49ab-b924-5b903a309a33/frame98/dhdl98.xvg 31c4f888-19a1-49ab-b924-5b903a309a33/frame99/dhdl99.xvg -o /tmp/biobb/unitests_29/pmxanalyse/sandbox_1c4bd9fc-e3c2-41fb-b4b6-b3e436250bcd/result.txt -w /tmp/biobb/unitests_29/pmxanalyse/sandbox_1c4bd9fc-e3c2-41fb-b4b6-b3e436250bcd/plot.png -m CGI BAR JARZ -t 298.15 -n 1 --skip 1 --prec 2 --units kJ --nbins 20 --dpi 600\n\n2024-11-04 14:30:07,468 [MainThread  ] [INFO ]  Executing: pmx analyse -fA 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame0/dhdl0.xvg 33499a5b-e...\n2024-11-04 14:30:07,468 [MainThread  ] [INFO ]  Exit code: 0\n2024-11-04 14:30:07,468 [MainThread  ] [INFO ]  \n\n ========================================================\n                   PROCESSING THE DATA\n ========================================================\n  Forward Data\n    First accepted file: 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame0/dhdl0.xvg\n    # data points: 25001\n    Length of trajectory:   50.000 ps\n    Delta lambda:  0.00004\n\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame1/dhdl1.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame2/dhdl2.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame3/dhdl3.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame4/dhdl4.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame5/dhdl5.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame6/dhdl6.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame7/dhdl7.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame8/dhdl8.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame9/dhdl9.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame10/dhdl10.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame11/dhdl11.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame12/dhdl12.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame13/dhdl13.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame14/dhdl14.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame15/dhdl15.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame16/dhdl16.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame17/dhdl17.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame18/dhdl18.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame19/dhdl19.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame20/dhdl20.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame21/dhdl21.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame22/dhdl22.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame23/dhdl23.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame24/dhdl24.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame25/dhdl25.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame26/dhdl26.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame27/dhdl27.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame28/dhdl28.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame29/dhdl29.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame30/dhdl30.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame31/dhdl31.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame32/dhdl32.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame33/dhdl33.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame34/dhdl34.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame35/dhdl35.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame36/dhdl36.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame37/dhdl37.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame38/dhdl38.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame39/dhdl39.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame40/dhdl40.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame41/dhdl41.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame42/dhdl42.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame43/dhdl43.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame44/dhdl44.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame45/dhdl45.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame46/dhdl46.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame47/dhdl47.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame48/dhdl48.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame49/dhdl49.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame50/dhdl50.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame51/dhdl51.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame52/dhdl52.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame53/dhdl53.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame54/dhdl54.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame55/dhdl55.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame56/dhdl56.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame57/dhdl57.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame58/dhdl58.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame59/dhdl59.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame60/dhdl60.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame61/dhdl61.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame62/dhdl62.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame63/dhdl63.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame64/dhdl64.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame65/dhdl65.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame66/dhdl66.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame67/dhdl67.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame68/dhdl68.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame69/dhdl69.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame70/dhdl70.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame71/dhdl71.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame72/dhdl72.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame73/dhdl73.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame74/dhdl74.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame75/dhdl75.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame76/dhdl76.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame77/dhdl77.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame78/dhdl78.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame79/dhdl79.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame80/dhdl80.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame81/dhdl81.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame82/dhdl82.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame83/dhdl83.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame84/dhdl84.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame85/dhdl85.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame86/dhdl86.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame87/dhdl87.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame88/dhdl88.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame89/dhdl89.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame90/dhdl90.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame91/dhdl91.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame92/dhdl92.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame93/dhdl93.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame94/dhdl94.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame95/dhdl95.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame96/dhdl96.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame97/dhdl97.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame98/dhdl98.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame99/dhdl99.xvg\n\n  Reverse Data\n    First accepted file: 31c4f888-19a1-49ab-b924-5b903a309a33/frame0/dhdl0.xvg\n    # data points: 25001\n    Length of trajectory:   50.000 ps\n    Delta lambda: -0.00004\n\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame1/dhdl1.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame2/dhdl2.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame3/dhdl3.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame4/dhdl4.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame5/dhdl5.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame6/dhdl6.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame7/dhdl7.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame8/dhdl8.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame9/dhdl9.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame10/dhdl10.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame11/dhdl11.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame12/dhdl12.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame13/dhdl13.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame14/dhdl14.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame15/dhdl15.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame16/dhdl16.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame17/dhdl17.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame18/dhdl18.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame19/dhdl19.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame20/dhdl20.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame21/dhdl21.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame22/dhdl22.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame23/dhdl23.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame24/dhdl24.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame25/dhdl25.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame26/dhdl26.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame27/dhdl27.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame28/dhdl28.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame29/dhdl29.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame30/dhdl30.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame31/dhdl31.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame32/dhdl32.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame33/dhdl33.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame34/dhdl34.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame35/dhdl35.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame36/dhdl36.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame37/dhdl37.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame38/dhdl38.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame39/dhdl39.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame40/dhdl40.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame41/dhdl41.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame42/dhdl42.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame43/dhdl43.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame44/dhdl44.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame45/dhdl45.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame46/dhdl46.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame47/dhdl47.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame48/dhdl48.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame49/dhdl49.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame50/dhdl50.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame51/dhdl51.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame52/dhdl52.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame53/dhdl53.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame54/dhdl54.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame55/dhdl55.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame56/dhdl56.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame57/dhdl57.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame58/dhdl58.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame59/dhdl59.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame60/dhdl60.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame61/dhdl61.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame62/dhdl62.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame63/dhdl63.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame64/dhdl64.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame65/dhdl65.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame66/dhdl66.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame67/dhdl67.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame68/dhdl68.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame69/dhdl69.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame70/dhdl70.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame71/dhdl71.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame72/dhdl72.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame73/dhdl73.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame74/dhdl74.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame75/dhdl75.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame76/dhdl76.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame77/dhdl77.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame78/dhdl78.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame79/dhdl79.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame80/dhdl80.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame81/dhdl81.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame82/dhdl82.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame83/dhdl83.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame84/dhdl84.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame85/dhdl85.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame86/dhdl86.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame87/dhdl87.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame88/dhdl88.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame89/dhdl89.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame90/dhdl90.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame91/dhdl91.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame92/dhdl92.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame93/dhdl93.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame94/dhdl94.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame95/dhdl95.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame96/dhdl96.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame97/dhdl97.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame98/dhdl98.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame99/dhdl99.xvg\n\n ========================================================\n                       ANALYSIS\n ========================================================\n  Number of forward (0-&amp;gt;1) trajectories: 100\n  Number of reverse (1-&amp;gt;0) trajectories: 100\n  Temperature : 298.15 K\n\n --------------------------------------------------------\n             Crooks Gaussian Intersection     \n --------------------------------------------------------\n  Calculating Intersection...\n\r  Bootstrap (Std Err): iteration 1/100\r  Bootstrap (Std Err): iteration 2/100\r  Bootstrap (Std Err): iteration 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Forward Gauss mean =    13.51 kJ/mol std =     4.03 kJ/mol\n  CGI: Reverse Gauss mean =     5.40 kJ/mol std =     8.49 kJ/mol\n  CGI: dG =     8.39 kJ/mol\n  CGI: Std Err (bootstrap:parametric) =     0.41 kJ/mol\n  CGI: Std Err (bootstrap) =     0.42 kJ/mol\n\n  Running KS-test...\n    Forward: gaussian quality = 0.41\n             ---&amp;gt; KS-Test Ok\n    Reverse: gaussian quality = 0.98\n             ---&amp;gt; KS-Test Ok\n\n --------------------------------------------------------\n             Bennett Acceptance Ratio     \n --------------------------------------------------------\n  Running Nelder-Mead Simplex algorithm... \n\r  Bootstrap (Std Err): iteration 1/100\r  Bootstrap (Std Err): iteration 2/100\r  Bootstrap (Std Err): iteration 3/100\r  Bootstrap (Std Err): iteration 4/100\r  Bootstrap (Std Err): iteration 5/100\r  Bootstrap (Std Err): iteration 6/100\r  Bootstrap (Std Err): iteration 7/100\r  Bootstrap (Std Err): iteration 8/100\r  Bootstrap (Std Err): iteration 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Bootstrap (Std Err): iteration 98/100\r  Bootstrap (Std Err): iteration 99/100\r  Bootstrap (Std Err): iteration 100/100\n  JARZ: dG Forward =    10.24 kJ/mol\n  JARZ: dG Reverse =    20.82 kJ/mol\n  JARZ: dG Mean    =    15.53 kJ/mol\n  JARZ: Std Err Forward (bootstrap) =     0.50 kJ/mol\n  JARZ: Std Err Reverse (bootstrap) =     2.36 kJ/mol\n\r  Bootstrap (Std Err): iteration 1/100\r  Bootstrap (Std Err): iteration 2/100\r  Bootstrap (Std Err): iteration 3/100\r  Bootstrap (Std Err): iteration 4/100\r  Bootstrap (Std Err): iteration 5/100\r  Bootstrap (Std Err): iteration 6/100\r  Bootstrap (Std Err): iteration 7/100\r  Bootstrap (Std Err): iteration 8/100\r  Bootstrap (Std Err): iteration 9/100\r  Bootstrap (Std Err): iteration 10/100\r  Bootstrap (Std Err): iteration 11/100\r  Bootstrap (Std Err): iteration 12/100\r  Bootstrap (Std Err): iteration 13/100\r  Bootstrap (Std Err): iteration 14/100\r  Bootstrap (Std Err): iteration 15/100\r  Bootstrap (Std Err): iteration 16/100\r  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Bootstrap (Std Err): iteration 63/100\r  Bootstrap (Std Err): iteration 64/100\r  Bootstrap (Std Err): iteration 65/100\r  Bootstrap (Std Err): iteration 66/100\r  Bootstrap (Std Err): iteration 67/100\r  Bootstrap (Std Err): iteration 68/100\r  Bootstrap (Std Err): iteration 69/100\r  Bootstrap (Std Err): iteration 70/100\r  Bootstrap (Std Err): iteration 71/100\r  Bootstrap (Std Err): iteration 72/100\r  Bootstrap (Std Err): iteration 73/100\r  Bootstrap (Std Err): iteration 74/100\r  Bootstrap (Std Err): iteration 75/100\r  Bootstrap (Std Err): iteration 76/100\r  Bootstrap (Std Err): iteration 77/100\r  Bootstrap (Std Err): iteration 78/100\r  Bootstrap (Std Err): iteration 79/100\r  Bootstrap (Std Err): iteration 80/100\r  Bootstrap (Std Err): iteration 81/100\r  Bootstrap (Std Err): iteration 82/100\r  Bootstrap (Std Err): iteration 83/100\r  Bootstrap (Std Err): iteration 84/100\r  Bootstrap (Std Err): iteration 85/100\r  Bootstrap (Std Err): iteration 86/100\r  Bootstrap (Std Err): iteration 87/100\r  Bootstrap (Std Err): iteration 88/100\r  Bootstrap (Std Err): iteration 89/100\r  Bootstrap (Std Err): iteration 90/100\r  Bootstrap (Std Err): iteration 91/100\r  Bootstrap (Std Err): iteration 92/100\r  Bootstrap (Std Err): iteration 93/100\r  Bootstrap (Std Err): iteration 94/100\r  Bootstrap (Std Err): iteration 95/100\r  Bootstrap (Std Err): iteration 96/100\r  Bootstrap (Std Err): iteration 97/100\r  Bootstrap (Std Err): iteration 98/100\r  Bootstrap (Std Err): iteration 99/100\r  Bootstrap (Std Err): iteration 100/100\n  JARZ_Gauss: dG Forward =    10.19 kJ/mol\n  JARZ_Gauss: dG Reverse =    20.07 kJ/mol\n  JARZ_Gauss: dG Mean    =    15.13 kJ/mol\n  JARZ_Gauss: Std Err (analytical) Forward =     0.62 kJ/mol\n  JARZ_Gauss: Std Err (analytical) Reverse =     2.25 kJ/mol\n  JARZ_Gauss: Std Err Forward (bootstrap) =     0.65 kJ/mol\n  JARZ_Gauss: Std Err Reverse (bootstrap) =     2.33 kJ/mol\n ========================================================\n\n   Plotting histograms......\n\n   ......done...........\n\n   Execution time = 00:00:10\n\n\n2024-11-04 14:30:07,491 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_29/pmxanalyse/sandbox_1c4bd9fc-e3c2-41fb-b4b6-b3e436250bcd&amp;#x27;, &amp;#x27;33499a5b-e3a8-4e42-999a-e027f462b9cc&amp;#x27;, &amp;#x27;31c4f888-19a1-49ab-b924-5b903a309a33&amp;#x27;]\n2024-11-04 14:30:07,492 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_29/pmxanalyse/result.txt\nChecking if empty file: /tmp/biobb/unitests_29/pmxanalyse/plot.png\nComparing images of both files:\n     IMAGE_A: /tmp/biobb/unitests_29/pmxanalyse/plot.png\n     IMAGE_B: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/reference/pmx/ref_plot.png\n     IMAGE_A HASH: ffdfe78183a7f7df SIZE: 64 bits\n     IMAGE_B HASH: ffdfe78183a7f7df SIZE: 64 bits\n     TOLERANCE: 1.0%, ABS TOLERANCE: 1 bits, DIFFERENCE: 0 bits\n\n------------------------------ Captured log call 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31c4f888-19a1-49ab-b924-5b903a309a33/frame47/dhdl47.xvg 31c4f888-19a1-49ab-b924-5b903a309a33/frame48/dhdl48.xvg 31c4f888-19a1-49ab-b924-5b903a309a33/frame49/dhdl49.xvg 31c4f888-19a1-49ab-b924-5b903a309a33/frame5/dhdl5.xvg 31c4f888-19a1-49ab-b924-5b903a309a33/frame50/dhdl50.xvg 31c4f888-19a1-49ab-b924-5b903a309a33/frame51/dhdl51.xvg 31c4f888-19a1-49ab-b924-5b903a309a33/frame52/dhdl52.xvg 31c4f888-19a1-49ab-b924-5b903a309a33/frame53/dhdl53.xvg 31c4f888-19a1-49ab-b924-5b903a309a33/frame54/dhdl54.xvg 31c4f888-19a1-49ab-b924-5b903a309a33/frame55/dhdl55.xvg 31c4f888-19a1-49ab-b924-5b903a309a33/frame56/dhdl56.xvg 31c4f888-19a1-49ab-b924-5b903a309a33/frame57/dhdl57.xvg 31c4f888-19a1-49ab-b924-5b903a309a33/frame58/dhdl58.xvg 31c4f888-19a1-49ab-b924-5b903a309a33/frame59/dhdl59.xvg 31c4f888-19a1-49ab-b924-5b903a309a33/frame6/dhdl6.xvg 31c4f888-19a1-49ab-b924-5b903a309a33/frame60/dhdl60.xvg 31c4f888-19a1-49ab-b924-5b903a309a33/frame61/dhdl61.xvg 31c4f888-19a1-49ab-b924-5b903a309a33/frame62/dhdl62.xvg 31c4f888-19a1-49ab-b924-5b903a309a33/frame63/dhdl63.xvg 31c4f888-19a1-49ab-b924-5b903a309a33/frame64/dhdl64.xvg 31c4f888-19a1-49ab-b924-5b903a309a33/frame65/dhdl65.xvg 31c4f888-19a1-49ab-b924-5b903a309a33/frame66/dhdl66.xvg 31c4f888-19a1-49ab-b924-5b903a309a33/frame67/dhdl67.xvg 31c4f888-19a1-49ab-b924-5b903a309a33/frame68/dhdl68.xvg 31c4f888-19a1-49ab-b924-5b903a309a33/frame69/dhdl69.xvg 31c4f888-19a1-49ab-b924-5b903a309a33/frame7/dhdl7.xvg 31c4f888-19a1-49ab-b924-5b903a309a33/frame70/dhdl70.xvg 31c4f888-19a1-49ab-b924-5b903a309a33/frame71/dhdl71.xvg 31c4f888-19a1-49ab-b924-5b903a309a33/frame72/dhdl72.xvg 31c4f888-19a1-49ab-b924-5b903a309a33/frame73/dhdl73.xvg 31c4f888-19a1-49ab-b924-5b903a309a33/frame74/dhdl74.xvg 31c4f888-19a1-49ab-b924-5b903a309a33/frame75/dhdl75.xvg 31c4f888-19a1-49ab-b924-5b903a309a33/frame76/dhdl76.xvg 31c4f888-19a1-49ab-b924-5b903a309a33/frame77/dhdl77.xvg 31c4f888-19a1-49ab-b924-5b903a309a33/frame78/dhdl78.xvg 31c4f888-19a1-49ab-b924-5b903a309a33/frame79/dhdl79.xvg 31c4f888-19a1-49ab-b924-5b903a309a33/frame8/dhdl8.xvg 31c4f888-19a1-49ab-b924-5b903a309a33/frame80/dhdl80.xvg 31c4f888-19a1-49ab-b924-5b903a309a33/frame81/dhdl81.xvg 31c4f888-19a1-49ab-b924-5b903a309a33/frame82/dhdl82.xvg 31c4f888-19a1-49ab-b924-5b903a309a33/frame83/dhdl83.xvg 31c4f888-19a1-49ab-b924-5b903a309a33/frame84/dhdl84.xvg 31c4f888-19a1-49ab-b924-5b903a309a33/frame85/dhdl85.xvg 31c4f888-19a1-49ab-b924-5b903a309a33/frame86/dhdl86.xvg 31c4f888-19a1-49ab-b924-5b903a309a33/frame87/dhdl87.xvg 31c4f888-19a1-49ab-b924-5b903a309a33/frame88/dhdl88.xvg 31c4f888-19a1-49ab-b924-5b903a309a33/frame89/dhdl89.xvg 31c4f888-19a1-49ab-b924-5b903a309a33/frame9/dhdl9.xvg 31c4f888-19a1-49ab-b924-5b903a309a33/frame90/dhdl90.xvg 31c4f888-19a1-49ab-b924-5b903a309a33/frame91/dhdl91.xvg 31c4f888-19a1-49ab-b924-5b903a309a33/frame92/dhdl92.xvg 31c4f888-19a1-49ab-b924-5b903a309a33/frame93/dhdl93.xvg 31c4f888-19a1-49ab-b924-5b903a309a33/frame94/dhdl94.xvg 31c4f888-19a1-49ab-b924-5b903a309a33/frame95/dhdl95.xvg 31c4f888-19a1-49ab-b924-5b903a309a33/frame96/dhdl96.xvg 31c4f888-19a1-49ab-b924-5b903a309a33/frame97/dhdl97.xvg 31c4f888-19a1-49ab-b924-5b903a309a33/frame98/dhdl98.xvg 31c4f888-19a1-49ab-b924-5b903a309a33/frame99/dhdl99.xvg -o /tmp/biobb/unitests_29/pmxanalyse/sandbox_1c4bd9fc-e3c2-41fb-b4b6-b3e436250bcd/result.txt -w /tmp/biobb/unitests_29/pmxanalyse/sandbox_1c4bd9fc-e3c2-41fb-b4b6-b3e436250bcd/plot.png -m CGI BAR JARZ -t 298.15 -n 1 --skip 1 --prec 2 --units kJ --nbins 20 --dpi 600\n\nINFO     /tmp/biobb/unitests_29/pmxanalyse/pmxanalyse_log.out:cmd_wrapper.py:36 Executing: pmx analyse -fA 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame0/dhdl0.xvg 33499a5b-e...\nINFO     /tmp/biobb/unitests_29/pmxanalyse/pmxanalyse_log.out:cmd_wrapper.py:37 Exit code: 0\nINFO     /tmp/biobb/unitests_29/pmxanalyse/pmxanalyse_log.out:cmd_wrapper.py:41 \n\n ========================================================\n                   PROCESSING THE DATA\n ========================================================\n  Forward Data\n    First accepted file: 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame0/dhdl0.xvg\n    # data points: 25001\n    Length of trajectory:   50.000 ps\n    Delta lambda:  0.00004\n\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame1/dhdl1.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame2/dhdl2.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame3/dhdl3.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame4/dhdl4.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame5/dhdl5.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame6/dhdl6.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame7/dhdl7.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame8/dhdl8.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame9/dhdl9.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame10/dhdl10.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame11/dhdl11.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame12/dhdl12.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame13/dhdl13.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame14/dhdl14.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame15/dhdl15.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame16/dhdl16.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame17/dhdl17.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame18/dhdl18.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame19/dhdl19.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame20/dhdl20.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame21/dhdl21.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame22/dhdl22.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame23/dhdl23.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame24/dhdl24.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame25/dhdl25.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame26/dhdl26.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame27/dhdl27.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame28/dhdl28.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame29/dhdl29.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame30/dhdl30.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame31/dhdl31.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame32/dhdl32.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame33/dhdl33.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame34/dhdl34.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame35/dhdl35.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame36/dhdl36.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame37/dhdl37.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame38/dhdl38.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame39/dhdl39.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame40/dhdl40.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame41/dhdl41.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame42/dhdl42.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame43/dhdl43.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame44/dhdl44.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame45/dhdl45.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame46/dhdl46.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame47/dhdl47.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame48/dhdl48.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame49/dhdl49.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame50/dhdl50.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame51/dhdl51.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame52/dhdl52.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame53/dhdl53.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame54/dhdl54.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame55/dhdl55.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame56/dhdl56.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame57/dhdl57.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame58/dhdl58.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame59/dhdl59.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame60/dhdl60.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame61/dhdl61.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame62/dhdl62.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame63/dhdl63.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame64/dhdl64.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame65/dhdl65.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame66/dhdl66.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame67/dhdl67.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame68/dhdl68.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame69/dhdl69.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame70/dhdl70.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame71/dhdl71.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame72/dhdl72.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame73/dhdl73.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame74/dhdl74.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame75/dhdl75.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame76/dhdl76.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame77/dhdl77.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame78/dhdl78.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame79/dhdl79.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame80/dhdl80.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame81/dhdl81.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame82/dhdl82.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame83/dhdl83.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame84/dhdl84.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame85/dhdl85.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame86/dhdl86.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame87/dhdl87.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame88/dhdl88.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame89/dhdl89.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame90/dhdl90.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame91/dhdl91.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame92/dhdl92.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame93/dhdl93.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame94/dhdl94.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame95/dhdl95.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame96/dhdl96.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame97/dhdl97.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame98/dhdl98.xvg\r    Reading 33499a5b-e3a8-4e42-999a-e027f462b9cc/frame99/dhdl99.xvg\n\n  Reverse Data\n    First accepted file: 31c4f888-19a1-49ab-b924-5b903a309a33/frame0/dhdl0.xvg\n    # data points: 25001\n    Length of trajectory:   50.000 ps\n    Delta lambda: -0.00004\n\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame1/dhdl1.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame2/dhdl2.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame3/dhdl3.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame4/dhdl4.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame5/dhdl5.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame6/dhdl6.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame7/dhdl7.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame8/dhdl8.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame9/dhdl9.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame10/dhdl10.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame11/dhdl11.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame12/dhdl12.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame13/dhdl13.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame14/dhdl14.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame15/dhdl15.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame16/dhdl16.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame17/dhdl17.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame18/dhdl18.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame19/dhdl19.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame20/dhdl20.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame21/dhdl21.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame22/dhdl22.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame23/dhdl23.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame24/dhdl24.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame25/dhdl25.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame26/dhdl26.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame27/dhdl27.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame28/dhdl28.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame29/dhdl29.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame30/dhdl30.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame31/dhdl31.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame32/dhdl32.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame33/dhdl33.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame34/dhdl34.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame35/dhdl35.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame36/dhdl36.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame37/dhdl37.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame38/dhdl38.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame39/dhdl39.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame40/dhdl40.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame41/dhdl41.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame42/dhdl42.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame43/dhdl43.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame44/dhdl44.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame45/dhdl45.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame46/dhdl46.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame47/dhdl47.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame48/dhdl48.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame49/dhdl49.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame50/dhdl50.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame51/dhdl51.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame52/dhdl52.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame53/dhdl53.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame54/dhdl54.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame55/dhdl55.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame56/dhdl56.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame57/dhdl57.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame58/dhdl58.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame59/dhdl59.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame60/dhdl60.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame61/dhdl61.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame62/dhdl62.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame63/dhdl63.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame64/dhdl64.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame65/dhdl65.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame66/dhdl66.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame67/dhdl67.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame68/dhdl68.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame69/dhdl69.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame70/dhdl70.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame71/dhdl71.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame72/dhdl72.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame73/dhdl73.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame74/dhdl74.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame75/dhdl75.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame76/dhdl76.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame77/dhdl77.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame78/dhdl78.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame79/dhdl79.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame80/dhdl80.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame81/dhdl81.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame82/dhdl82.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame83/dhdl83.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame84/dhdl84.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame85/dhdl85.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame86/dhdl86.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame87/dhdl87.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame88/dhdl88.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame89/dhdl89.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame90/dhdl90.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame91/dhdl91.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame92/dhdl92.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame93/dhdl93.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame94/dhdl94.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame95/dhdl95.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame96/dhdl96.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame97/dhdl97.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame98/dhdl98.xvg\r    Reading 31c4f888-19a1-49ab-b924-5b903a309a33/frame99/dhdl99.xvg\n\n ========================================================\n                       ANALYSIS\n ========================================================\n  Number of forward (0-&amp;gt;1) trajectories: 100\n  Number of reverse (1-&amp;gt;0) trajectories: 100\n  Temperature : 298.15 K\n\n --------------------------------------------------------\n             Crooks Gaussian Intersection     \n --------------------------------------------------------\n  Calculating Intersection...\n\r  Bootstrap (Std Err): iteration 1/100\r  Bootstrap (Std Err): iteration 2/100\r  Bootstrap (Std Err): iteration 3/100\r  Bootstrap (Std Err): iteration 4/100\r  Bootstrap (Std Err): iteration 5/100\r  Bootstrap (Std Err): iteration 6/100\r  Bootstrap (Std Err): iteration 7/100\r  Bootstrap (Std Err): iteration 8/100\r  Bootstrap (Std Err): iteration 9/100\r  Bootstrap (Std Err): iteration 10/100\r  Bootstrap (Std Err): iteration 11/100\r  Bootstrap (Std Err): iteration 12/100\r  Bootstrap (Std Err): iteration 13/100\r  Bootstrap (Std Err): iteration 14/100\r  Bootstrap (Std Err): iteration 15/100\r  Bootstrap (Std Err): iteration 16/100\r  Bootstrap (Std Err): iteration 17/100\r  Bootstrap (Std Err): iteration 18/100\r  Bootstrap (Std Err): iteration 19/100\r  Bootstrap (Std Err): iteration 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Err): iteration 69/100\r  Bootstrap (Std Err): iteration 70/100\r  Bootstrap (Std Err): iteration 71/100\r  Bootstrap (Std Err): iteration 72/100\r  Bootstrap (Std Err): iteration 73/100\r  Bootstrap (Std Err): iteration 74/100\r  Bootstrap (Std Err): iteration 75/100\r  Bootstrap (Std Err): iteration 76/100\r  Bootstrap (Std Err): iteration 77/100\r  Bootstrap (Std Err): iteration 78/100\r  Bootstrap (Std Err): iteration 79/100\r  Bootstrap (Std Err): iteration 80/100\r  Bootstrap (Std Err): iteration 81/100\r  Bootstrap (Std Err): iteration 82/100\r  Bootstrap (Std Err): iteration 83/100\r  Bootstrap (Std Err): iteration 84/100\r  Bootstrap (Std Err): iteration 85/100\r  Bootstrap (Std Err): iteration 86/100\r  Bootstrap (Std Err): iteration 87/100\r  Bootstrap (Std Err): iteration 88/100\r  Bootstrap (Std Err): iteration 89/100\r  Bootstrap (Std Err): iteration 90/100\r  Bootstrap (Std Err): iteration 91/100\r  Bootstrap (Std Err): iteration 92/100\r  Bootstrap (Std Err): iteration 93/100\r  Bootstrap (Std Err): iteration 94/100\r  Bootstrap (Std Err): iteration 95/100\r  Bootstrap (Std Err): iteration 96/100\r  Bootstrap (Std Err): iteration 97/100\r  Bootstrap (Std Err): iteration 98/100\r  Bootstrap (Std Err): iteration 99/100\r  Bootstrap (Std Err): iteration 100/100\n  CGI: Forward Gauss mean =    13.51 kJ/mol std =     4.03 kJ/mol\n  CGI: Reverse Gauss mean =     5.40 kJ/mol std =     8.49 kJ/mol\n  CGI: dG =     8.39 kJ/mol\n  CGI: Std Err (bootstrap:parametric) =     0.41 kJ/mol\n  CGI: Std Err (bootstrap) =     0.42 kJ/mol\n\n  Running KS-test...\n    Forward: gaussian quality = 0.41\n             ---&amp;gt; KS-Test Ok\n    Reverse: gaussian quality = 0.98\n             ---&amp;gt; KS-Test Ok\n\n --------------------------------------------------------\n             Bennett Acceptance Ratio     \n --------------------------------------------------------\n  Running Nelder-Mead Simplex algorithm... \n\r  Bootstrap (Std Err): iteration 1/100\r  Bootstrap 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99/100\r  Bootstrap (Std Err): iteration 100/100\n\r  Bootstrap (Conv): iteration 1/100\r  Bootstrap (Conv): iteration 2/100\r  Bootstrap (Conv): iteration 3/100\r  Bootstrap (Conv): iteration 4/100\r  Bootstrap (Conv): iteration 5/100\r  Bootstrap (Conv): iteration 6/100\r  Bootstrap (Conv): iteration 7/100\r  Bootstrap (Conv): iteration 8/100\r  Bootstrap (Conv): iteration 9/100\r  Bootstrap (Conv): iteration 10/100\r  Bootstrap (Conv): iteration 11/100\r  Bootstrap (Conv): iteration 12/100\r  Bootstrap (Conv): iteration 13/100\r  Bootstrap (Conv): iteration 14/100\r  Bootstrap (Conv): iteration 15/100\r  Bootstrap (Conv): iteration 16/100\r  Bootstrap (Conv): iteration 17/100\r  Bootstrap (Conv): iteration 18/100\r  Bootstrap (Conv): iteration 19/100\r  Bootstrap (Conv): iteration 20/100\r  Bootstrap (Conv): iteration 21/100\r  Bootstrap (Conv): iteration 22/100\r  Bootstrap (Conv): iteration 23/100\r  Bootstrap (Conv): iteration 24/100\r  Bootstrap (Conv): iteration 25/100\r  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-0.23\n  BAR: Conv Std Err (bootstrap) =     0.04\n\n --------------------------------------------------------\n             Jarzynski estimator     \n --------------------------------------------------------\n\r  Bootstrap (Std Err): iteration 1/100\r  Bootstrap (Std Err): iteration 2/100\r  Bootstrap (Std Err): iteration 3/100\r  Bootstrap (Std Err): iteration 4/100\r  Bootstrap (Std Err): iteration 5/100\r  Bootstrap (Std Err): iteration 6/100\r  Bootstrap (Std Err): iteration 7/100\r  Bootstrap (Std Err): iteration 8/100\r  Bootstrap (Std Err): iteration 9/100\r  Bootstrap (Std Err): iteration 10/100\r  Bootstrap (Std Err): iteration 11/100\r  Bootstrap (Std Err): iteration 12/100\r  Bootstrap (Std Err): iteration 13/100\r  Bootstrap (Std Err): iteration 14/100\r  Bootstrap (Std Err): iteration 15/100\r  Bootstrap (Std Err): iteration 16/100\r  Bootstrap (Std Err): iteration 17/100\r  Bootstrap (Std Err): iteration 18/100\r  Bootstrap (Std Err): iteration 19/100\r  Bootstrap (Std 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Bootstrap (Std Err): iteration 80/100\r  Bootstrap (Std Err): iteration 81/100\r  Bootstrap (Std Err): iteration 82/100\r  Bootstrap (Std Err): iteration 83/100\r  Bootstrap (Std Err): iteration 84/100\r  Bootstrap (Std Err): iteration 85/100\r  Bootstrap (Std Err): iteration 86/100\r  Bootstrap (Std Err): iteration 87/100\r  Bootstrap (Std Err): iteration 88/100\r  Bootstrap (Std Err): iteration 89/100\r  Bootstrap (Std Err): iteration 90/100\r  Bootstrap (Std Err): iteration 91/100\r  Bootstrap (Std Err): iteration 92/100\r  Bootstrap (Std Err): iteration 93/100\r  Bootstrap (Std Err): iteration 94/100\r  Bootstrap (Std Err): iteration 95/100\r  Bootstrap (Std Err): iteration 96/100\r  Bootstrap (Std Err): iteration 97/100\r  Bootstrap (Std Err): iteration 98/100\r  Bootstrap (Std Err): iteration 99/100\r  Bootstrap (Std Err): iteration 100/100\n  JARZ_Gauss: dG Forward =    10.19 kJ/mol\n  JARZ_Gauss: dG Reverse =    20.07 kJ/mol\n  JARZ_Gauss: dG Mean    =    15.13 kJ/mol\n  JARZ_Gauss: Std Err (analytical) Forward =     0.62 kJ/mol\n  JARZ_Gauss: Std Err (analytical) Reverse =     2.25 kJ/mol\n  JARZ_Gauss: Std Err Forward (bootstrap) =     0.65 kJ/mol\n  JARZ_Gauss: Std Err Reverse (bootstrap) =     2.33 kJ/mol\n ========================================================\n\n   Plotting histograms......\n\n   ......done...........\n\n   Execution time = 00:00:10\n\n\nINFO     /tmp/biobb/unitests_29/pmxanalyse/pmxanalyse_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_29/pmxanalyse/sandbox_1c4bd9fc-e3c2-41fb-b4b6-b3e436250bcd&amp;#x27;, &amp;#x27;33499a5b-e3a8-4e42-999a-e027f462b9cc&amp;#x27;, &amp;#x27;31c4f888-19a1-49ab-b924-5b903a309a33&amp;#x27;]\nINFO     /tmp/biobb/unitests_29/pmxanalyse/pmxanalyse_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_29\n&#34;}], &#34;biobb_pmx/test/unitests/test_pmx/test_pmxatom_mapping.py::TestPmxatom_mapping::test_pmxatom_mapping&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_pmx/test/unitests/test_pmx/test_pmxatom_mapping.py::TestPmxatom_mapping::test_pmxatom_mapping&#34;, &#34;duration&#34;: &#34;00:00:05&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_pmx/test/unitests/test_pmx/test_pmxatom_mapping.py::TestPmxatom_mapping::test_pmxatom_mapping&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:00:05&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-11-04 14:30:08,149 [MainThread  ] [INFO ]  Module: biobb_pmx.pmxbiobb.pmxatom_mapping Version: 4.2.1\n2024-11-04 14:30:08,149 [MainThread  ] [INFO ]  /tmp/biobb/unitests_29/pmxatom_mapping/sandbox_d7655c3c-f08a-4824-9722-d029dc5a004b directory successfully created\n2024-11-04 14:30:08,149 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/lig1.pdb to /tmp/biobb/unitests_29/pmxatom_mapping/sandbox_d7655c3c-f08a-4824-9722-d029dc5a004b\n2024-11-04 14:30:08,150 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/lig2.pdb to /tmp/biobb/unitests_29/pmxatom_mapping/sandbox_d7655c3c-f08a-4824-9722-d029dc5a004b\n2024-11-04 14:30:08,150 [MainThread  ] [INFO ]  pmx atomMapping -i1 /tmp/biobb/unitests_29/pmxatom_mapping/sandbox_d7655c3c-f08a-4824-9722-d029dc5a004b/lig1.pdb -i2 /tmp/biobb/unitests_29/pmxatom_mapping/sandbox_d7655c3c-f08a-4824-9722-d029dc5a004b/lig2.pdb -o1 /tmp/biobb/unitests_29/pmxatom_mapping/sandbox_d7655c3c-f08a-4824-9722-d029dc5a004b/pairs1.dat -o2 /tmp/biobb/unitests_29/pmxatom_mapping/sandbox_d7655c3c-f08a-4824-9722-d029dc5a004b/pairs2.dat -log /tmp/biobb/unitests_29/pmxatom_mapping/sandbox_d7655c3c-f08a-4824-9722-d029dc5a004b/atom_mapping.log --d 0.05\n\n2024-11-04 14:30:12,665 [MainThread  ] [INFO ]  Executing: pmx atomMapping -i1 /tmp/biobb/unitests_29/pmxatom_mapping/sandbox_d7655c3c-f08a...\n2024-11-04 14:30:12,666 [MainThread  ] [INFO ]  Exit code: 0\n2024-11-04 14:30:12,666 [MainThread  ] [INFO ]  atomMapping__log_&amp;gt; Morphable atoms will be identified using the following methods:\natomMapping__log_&amp;gt; Alignment: True\natomMapping__log_&amp;gt; MCS: True\natomMapping__log_&amp;gt; Initializing the main LigandsAtomMapping object\natomMapping__log_&amp;gt; The topology matching approach will be used (MCS)\natomMapping__log_&amp;gt; fmcs module: Copyright (c) 2012 Andrew Dalke Scientific AB\natomMapping__log_&amp;gt; MCS: trying to run an MCS using all atoms: modified molecules, match elements...\natomMapping__log_&amp;gt; MCS searching...\natomMapping__log_&amp;gt; Found 4 MCSs in total (mol1: 2, mol2: 2), each with 22 atoms and 23 bonds\natomMapping__log_&amp;gt; Chirality check.\natomMapping__log_&amp;gt; Avoiding breaking rings.\natomMapping__log_&amp;gt; Final MCS that survived after pruning: 33 atoms\natomMapping__log_&amp;gt; MCS: all atoms, modified molecules, size of mapping: 33\natomMapping__log_&amp;gt; MCS: trying to run an MCS using all atoms: unmodified molecules, match elements...\natomMapping__log_&amp;gt; MCS searching...\natomMapping__log_&amp;gt; Found 4 MCSs in total (mol1: 2, mol2: 2), each with 22 atoms and 23 bonds\natomMapping__log_&amp;gt; Chirality check.\natomMapping__log_&amp;gt; Avoiding breaking rings.\natomMapping__log_&amp;gt; Final MCS that survived after pruning: 33 atoms\natomMapping__log_&amp;gt; MCS: all atoms, unmodified molecules, size of mapping: 33\natomMapping__log_&amp;gt; MCS: trying to run an MCS using rings only...\natomMapping__log_&amp;gt; MCS searching...\natomMapping__log_&amp;gt; Found 576 MCSs in total (mol1: 24, mol2: 24), each with 6 atoms and 6 bonds\natomMapping__log_&amp;gt; Chirality check.\natomMapping__log_&amp;gt; Avoiding breaking rings.\natomMapping__log_&amp;gt; Final MCS that survived after pruning: 7 atoms\natomMapping__log_&amp;gt; MCS: using variant with the mapping size of 33\natomMapping__log_&amp;gt; The alignment approach will be used\natomMapping__log_&amp;gt; Tosco, P., Balle, T. &amp;amp; Shiri, F. Open3DALIGN: an open-source software aimed at unsupervised ligand alignment. J Comput Aided Mol Des 25:777-83 (2011)\natomMapping__log_&amp;gt; Alignment is based on atom logP contributions: S. A. Wildman and G. M. Crippen JCICS _39_ 868-873 (1999)\natomMapping__log_&amp;gt; Alignment: trying to align all atoms...\natomMapping__log_&amp;gt; Avoiding breaking rings.\natomMapping__log_&amp;gt; Alignment: size of mapping: 25\natomMapping__log_&amp;gt; Alignment: trying to align rings only...\natomMapping__log_&amp;gt; Avoiding breaking rings.\natomMapping__log_&amp;gt; Size of mapping: 31\natomMapping__log_&amp;gt; Alignment: using ring only alignment result.\natomMapping__log_&amp;gt; The final result is based on the MCS.\n\natomMapping__log_&amp;gt; Final results:\natomMapping__log_&amp;gt; Atoms considered in mol1: 39\natomMapping__log_&amp;gt; Atoms considered in mol2: 39\natomMapping__log_&amp;gt; Morphable atoms in both molecules: 33 33\natomMapping__log_&amp;gt; Dissimilarity (distance) score: 0.1538\n\n\n2024-11-04 14:30:12,667 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_29/pmxatom_mapping/sandbox_d7655c3c-f08a-4824-9722-d029dc5a004b&amp;#x27;]\n2024-11-04 14:30:12,667 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_29/pmxatom_mapping/pairs1.dat\nChecking if empty file: /tmp/biobb/unitests_29/pmxatom_mapping/pairs2.dat\nComparing: \n        File_A: /tmp/biobb/unitests_29/pmxatom_mapping/pairs1.dat\n        File_B: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/reference/pmx/ref_pairs1.dat\n        File_A hash: b&amp;#x27;r\\x0f\\xa3\\xb7,\\xd2D\\xcbo&amp;quot;.\\xc5o%\\x1fXD\\xce3\\xaf\\xb6\\xe4:V\\xae\\x04\\x1e\\x90Nd\\xf4\\x87&amp;#x27;\n        File_B hash: b&amp;#x27;r\\x0f\\xa3\\xb7,\\xd2D\\xcbo&amp;quot;.\\xc5o%\\x1fXD\\xce3\\xaf\\xb6\\xe4:V\\xae\\x04\\x1e\\x90Nd\\xf4\\x87&amp;#x27;\nComparing: \n        File_A: /tmp/biobb/unitests_29/pmxatom_mapping/pairs2.dat\n        File_B: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/reference/pmx/ref_pairs2.dat\n        File_A hash: b&amp;#x27;\\xc8|}\\xca\\xb4\\x1c\\x89\\xe3@W\\xd1\\xa7\\xe7\\x06\\xca\\xbb\\xae#M$6Z2\\xba\\xadXj\\x85\\xd1\\xa0\\xa8\\xad&amp;#x27;\n        File_B hash: b&amp;#x27;\\xc8|}\\xca\\xb4\\x1c\\x89\\xe3@W\\xd1\\xa7\\xe7\\x06\\xca\\xbb\\xae#M$6Z2\\xba\\xadXj\\x85\\xd1\\xa0\\xa8\\xad&amp;#x27;\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_29/pmxatom_mapping/pmxatom_mapping_log.out:file_utils.py:409 Module: biobb_pmx.pmxbiobb.pmxatom_mapping Version: 4.2.1\nINFO     /tmp/biobb/unitests_29/pmxatom_mapping/pmxatom_mapping_log.out:file_utils.py:82 /tmp/biobb/unitests_29/pmxatom_mapping/sandbox_d7655c3c-f08a-4824-9722-d029dc5a004b directory successfully created\nINFO     /tmp/biobb/unitests_29/pmxatom_mapping/pmxatom_mapping_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/lig1.pdb to /tmp/biobb/unitests_29/pmxatom_mapping/sandbox_d7655c3c-f08a-4824-9722-d029dc5a004b\nINFO     /tmp/biobb/unitests_29/pmxatom_mapping/pmxatom_mapping_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/lig2.pdb to /tmp/biobb/unitests_29/pmxatom_mapping/sandbox_d7655c3c-f08a-4824-9722-d029dc5a004b\nINFO     /tmp/biobb/unitests_29/pmxatom_mapping/pmxatom_mapping_log.out:cmd_wrapper.py:63 pmx atomMapping -i1 /tmp/biobb/unitests_29/pmxatom_mapping/sandbox_d7655c3c-f08a-4824-9722-d029dc5a004b/lig1.pdb -i2 /tmp/biobb/unitests_29/pmxatom_mapping/sandbox_d7655c3c-f08a-4824-9722-d029dc5a004b/lig2.pdb -o1 /tmp/biobb/unitests_29/pmxatom_mapping/sandbox_d7655c3c-f08a-4824-9722-d029dc5a004b/pairs1.dat -o2 /tmp/biobb/unitests_29/pmxatom_mapping/sandbox_d7655c3c-f08a-4824-9722-d029dc5a004b/pairs2.dat -log /tmp/biobb/unitests_29/pmxatom_mapping/sandbox_d7655c3c-f08a-4824-9722-d029dc5a004b/atom_mapping.log --d 0.05\n\nINFO     /tmp/biobb/unitests_29/pmxatom_mapping/pmxatom_mapping_log.out:cmd_wrapper.py:36 Executing: pmx atomMapping -i1 /tmp/biobb/unitests_29/pmxatom_mapping/sandbox_d7655c3c-f08a...\nINFO     /tmp/biobb/unitests_29/pmxatom_mapping/pmxatom_mapping_log.out:cmd_wrapper.py:37 Exit code: 0\nINFO     /tmp/biobb/unitests_29/pmxatom_mapping/pmxatom_mapping_log.out:cmd_wrapper.py:41 atomMapping__log_&amp;gt; Morphable atoms will be identified using the following methods:\natomMapping__log_&amp;gt; Alignment: True\natomMapping__log_&amp;gt; MCS: True\natomMapping__log_&amp;gt; Initializing the main LigandsAtomMapping object\natomMapping__log_&amp;gt; The topology matching approach will be used (MCS)\natomMapping__log_&amp;gt; fmcs module: Copyright (c) 2012 Andrew Dalke Scientific AB\natomMapping__log_&amp;gt; MCS: trying to run an MCS using all atoms: modified molecules, match elements...\natomMapping__log_&amp;gt; MCS searching...\natomMapping__log_&amp;gt; Found 4 MCSs in total (mol1: 2, mol2: 2), each with 22 atoms and 23 bonds\natomMapping__log_&amp;gt; Chirality check.\natomMapping__log_&amp;gt; Avoiding breaking rings.\natomMapping__log_&amp;gt; Final MCS that survived after pruning: 33 atoms\natomMapping__log_&amp;gt; MCS: all atoms, modified molecules, size of mapping: 33\natomMapping__log_&amp;gt; MCS: trying to run an MCS using all atoms: unmodified molecules, match elements...\natomMapping__log_&amp;gt; MCS searching...\natomMapping__log_&amp;gt; Found 4 MCSs in total (mol1: 2, mol2: 2), each with 22 atoms and 23 bonds\natomMapping__log_&amp;gt; Chirality check.\natomMapping__log_&amp;gt; Avoiding breaking rings.\natomMapping__log_&amp;gt; Final MCS that survived after pruning: 33 atoms\natomMapping__log_&amp;gt; MCS: all atoms, unmodified molecules, size of mapping: 33\natomMapping__log_&amp;gt; MCS: trying to run an MCS using rings only...\natomMapping__log_&amp;gt; MCS searching...\natomMapping__log_&amp;gt; Found 576 MCSs in total (mol1: 24, mol2: 24), each with 6 atoms and 6 bonds\natomMapping__log_&amp;gt; Chirality check.\natomMapping__log_&amp;gt; Avoiding breaking rings.\natomMapping__log_&amp;gt; Final MCS that survived after pruning: 7 atoms\natomMapping__log_&amp;gt; MCS: using variant with the mapping size of 33\natomMapping__log_&amp;gt; The alignment approach will be used\natomMapping__log_&amp;gt; Tosco, P., Balle, T. &amp;amp; Shiri, F. Open3DALIGN: an open-source software aimed at unsupervised ligand alignment. J Comput Aided Mol Des 25:777-83 (2011)\natomMapping__log_&amp;gt; Alignment is based on atom logP contributions: S. A. Wildman and G. M. Crippen JCICS _39_ 868-873 (1999)\natomMapping__log_&amp;gt; Alignment: trying to align all atoms...\natomMapping__log_&amp;gt; Avoiding breaking rings.\natomMapping__log_&amp;gt; Alignment: size of mapping: 25\natomMapping__log_&amp;gt; Alignment: trying to align rings only...\natomMapping__log_&amp;gt; Avoiding breaking rings.\natomMapping__log_&amp;gt; Size of mapping: 31\natomMapping__log_&amp;gt; Alignment: using ring only alignment result.\natomMapping__log_&amp;gt; The final result is based on the MCS.\n\natomMapping__log_&amp;gt; Final results:\natomMapping__log_&amp;gt; Atoms considered in mol1: 39\natomMapping__log_&amp;gt; Atoms considered in mol2: 39\natomMapping__log_&amp;gt; Morphable atoms in both molecules: 33 33\natomMapping__log_&amp;gt; Dissimilarity (distance) score: 0.1538\n\n\nINFO     /tmp/biobb/unitests_29/pmxatom_mapping/pmxatom_mapping_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_29/pmxatom_mapping/sandbox_d7655c3c-f08a-4824-9722-d029dc5a004b&amp;#x27;]\nINFO     /tmp/biobb/unitests_29/pmxatom_mapping/pmxatom_mapping_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_29\n&#34;}], &#34;biobb_pmx/test/unitests/test_pmx/test_pmxcreate_top.py::TestPmxcreate_top::test_pmxcreate_top&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_pmx/test/unitests/test_pmx/test_pmxcreate_top.py::TestPmxcreate_top::test_pmxcreate_top&#34;, &#34;duration&#34;: &#34;42 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_pmx/test/unitests/test_pmx/test_pmxcreate_top.py::TestPmxcreate_top::test_pmxcreate_top&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;42 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-11-04 14:30:12,700 [MainThread  ] [INFO ]  Module: biobb_pmx.pmxbiobb.pmxcreate_top Version: 4.2.1\n2024-11-04 14:30:12,700 [MainThread  ] [INFO ]  /tmp/biobb/unitests_29/pmxcreate_top/sandbox_23ac6958-dab3-4795-a439-f78373a647bd directory successfully created\n2024-11-04 14:30:12,700 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/topo1.itp to /tmp/biobb/unitests_29/pmxcreate_top/sandbox_23ac6958-dab3-4795-a439-f78373a647bd\n2024-11-04 14:30:12,700 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/topo2.itp to /tmp/biobb/unitests_29/pmxcreate_top/sandbox_23ac6958-dab3-4795-a439-f78373a647bd\n2024-11-04 14:30:12,700 [MainThread  ] [INFO ]  Running create_top from pmx package...\n\n2024-11-04 14:30:12,701 [MainThread  ] [INFO ]  Creating c3906d2e-476a-4793-864a-d8e193739dd3 temporary folder\n2024-11-04 14:30:12,701 [MainThread  ] [INFO ]  Creating topo1.itp itp file in temporary folder\n2024-11-04 14:30:12,701 [MainThread  ] [INFO ]  Creating topo2.itp itp file in temporary folder\n2024-11-04 14:30:12,701 [MainThread  ] [INFO ]  Compressing topology to: /tmp/biobb/unitests_29/pmxcreate_top/topo.zip\n2024-11-04 14:30:12,702 [MainThread  ] [INFO ]  Ignored file amber99sb-star-ildn-mut.ff/forcefield.itp\n2024-11-04 14:30:12,702 [MainThread  ] [INFO ]  Ignored file amber99sb-star-ildn-mut.ff/spce.itp\n2024-11-04 14:30:12,702 [MainThread  ] [INFO ]  Ignored file amber99sb-star-ildn-mut.ff/ions.itp\n2024-11-04 14:30:12,703 [MainThread  ] [INFO ]  Adding:\n2024-11-04 14:30:12,703 [MainThread  ] [INFO ]  [&amp;#x27;topo1.itp&amp;#x27;, &amp;#x27;topo2.itp&amp;#x27;, &amp;#x27;topology.top&amp;#x27;]\n2024-11-04 14:30:12,703 [MainThread  ] [INFO ]  to: /tmp/biobb/unitests_29/pmxcreate_top/topo.zip\n2024-11-04 14:30:12,704 [MainThread  ] [INFO ]  Removed: [&amp;#x27;topo1.itp&amp;#x27;, &amp;#x27;topo2.itp&amp;#x27;, &amp;#x27;topology.top&amp;#x27;]\n2024-11-04 14:30:12,704 [MainThread  ] [INFO ]  Exit code 0\n\n2024-11-04 14:30:12,704 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_29/pmxcreate_top/sandbox_23ac6958-dab3-4795-a439-f78373a647bd&amp;#x27;]\n2024-11-04 14:30:12,704 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_29/pmxcreate_top/topo.zip\nThis is a ZIP comparison!\nUnzipping:\nCreating a unique_dir for: /tmp/biobb/unitests_29/pmxcreate_top/topo.zip\nCreating a unique_dir for: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/reference/pmx/ref_hybridTopo.zip\nComparing TOP/ITP:\n     FILE_A: a9a77220-cf2d-4a23-84af-0a4d3954aad7/topo1.itp\n     FILE_B: 68c96dc2-83d8-42ba-a29e-60f934b0444d/topo1.itp\nComparing TOP/ITP:\n     FILE_A: a9a77220-cf2d-4a23-84af-0a4d3954aad7/topo2.itp\n     FILE_B: 68c96dc2-83d8-42ba-a29e-60f934b0444d/topo2.itp\nComparing TOP/ITP:\n     FILE_A: a9a77220-cf2d-4a23-84af-0a4d3954aad7/topology.top\n     FILE_B: 68c96dc2-83d8-42ba-a29e-60f934b0444d/topology.top\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_29/pmxcreate_top/pmxcreate_top_log.out:file_utils.py:409 Module: biobb_pmx.pmxbiobb.pmxcreate_top Version: 4.2.1\nINFO     /tmp/biobb/unitests_29/pmxcreate_top/pmxcreate_top_log.out:file_utils.py:82 /tmp/biobb/unitests_29/pmxcreate_top/sandbox_23ac6958-dab3-4795-a439-f78373a647bd directory successfully created\nINFO     /tmp/biobb/unitests_29/pmxcreate_top/pmxcreate_top_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/topo1.itp to /tmp/biobb/unitests_29/pmxcreate_top/sandbox_23ac6958-dab3-4795-a439-f78373a647bd\nINFO     /tmp/biobb/unitests_29/pmxcreate_top/pmxcreate_top_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/topo2.itp to /tmp/biobb/unitests_29/pmxcreate_top/sandbox_23ac6958-dab3-4795-a439-f78373a647bd\nINFO     /tmp/biobb/unitests_29/pmxcreate_top/pmxcreate_top_log.out:file_utils.py:409 Running create_top from pmx package...\n\nINFO     /tmp/biobb/unitests_29/pmxcreate_top/pmxcreate_top_log.out:file_utils.py:409 Creating c3906d2e-476a-4793-864a-d8e193739dd3 temporary folder\nINFO     /tmp/biobb/unitests_29/pmxcreate_top/pmxcreate_top_log.out:file_utils.py:409 Creating topo1.itp itp file in temporary folder\nINFO     /tmp/biobb/unitests_29/pmxcreate_top/pmxcreate_top_log.out:file_utils.py:409 Creating topo2.itp itp file in temporary folder\nINFO     /tmp/biobb/unitests_29/pmxcreate_top/pmxcreate_top_log.out:file_utils.py:409 Compressing topology to: /tmp/biobb/unitests_29/pmxcreate_top/topo.zip\nINFO     /tmp/biobb/unitests_29/pmxcreate_top/pmxcreate_top_log.out:file_utils.py:203 Ignored file amber99sb-star-ildn-mut.ff/forcefield.itp\nINFO     /tmp/biobb/unitests_29/pmxcreate_top/pmxcreate_top_log.out:file_utils.py:203 Ignored file amber99sb-star-ildn-mut.ff/spce.itp\nINFO     /tmp/biobb/unitests_29/pmxcreate_top/pmxcreate_top_log.out:file_utils.py:203 Ignored file amber99sb-star-ildn-mut.ff/ions.itp\nINFO     /tmp/biobb/unitests_29/pmxcreate_top/pmxcreate_top_log.out:file_utils.py:148 Adding:\nINFO     /tmp/biobb/unitests_29/pmxcreate_top/pmxcreate_top_log.out:file_utils.py:149 [&amp;#x27;topo1.itp&amp;#x27;, &amp;#x27;topo2.itp&amp;#x27;, &amp;#x27;topology.top&amp;#x27;]\nINFO     /tmp/biobb/unitests_29/pmxcreate_top/pmxcreate_top_log.out:file_utils.py:150 to: /tmp/biobb/unitests_29/pmxcreate_top/topo.zip\nINFO     /tmp/biobb/unitests_29/pmxcreate_top/pmxcreate_top_log.out:file_utils.py:409 Removed: [&amp;#x27;topo1.itp&amp;#x27;, &amp;#x27;topo2.itp&amp;#x27;, &amp;#x27;topology.top&amp;#x27;]\nINFO     /tmp/biobb/unitests_29/pmxcreate_top/pmxcreate_top_log.out:file_utils.py:409 Exit code 0\n\nINFO     /tmp/biobb/unitests_29/pmxcreate_top/pmxcreate_top_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_29/pmxcreate_top/sandbox_23ac6958-dab3-4795-a439-f78373a647bd&amp;#x27;]\nINFO     /tmp/biobb/unitests_29/pmxcreate_top/pmxcreate_top_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_29\n&#34;}], &#34;biobb_pmx/test/unitests/test_pmx/test_pmxgentop.py::TestPmxgentop::test_pmxgentop&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_pmx/test/unitests/test_pmx/test_pmxgentop.py::TestPmxgentop::test_pmxgentop&#34;, &#34;duration&#34;: &#34;00:00:07&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_pmx/test/unitests/test_pmx/test_pmxgentop.py::TestPmxgentop::test_pmxgentop&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:00:07&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-11-04 14:30:12,743 [MainThread  ] [INFO ]  Module: biobb_pmx.pmxbiobb.pmxgentop Version: 4.2.1\n2024-11-04 14:30:12,743 [MainThread  ] [INFO ]  /tmp/biobb/unitests_29/pmxgentop/sandbox_44db0fd9-cd06-4ac0-90db-66fc666d9b2e directory successfully created\n2024-11-04 14:30:12,745 [MainThread  ] [INFO ]  Extracting: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/mut_gmx.top.zip\n2024-11-04 14:30:12,745 [MainThread  ] [INFO ]  to:\n2024-11-04 14:30:12,745 [MainThread  ] [INFO ]  [&amp;#x27;6d36bade-c33c-405e-88a8-3da6b1f8a1b8/p2g.top&amp;#x27;, &amp;#x27;6d36bade-c33c-405e-88a8-3da6b1f8a1b8/p2g_Ion.itp&amp;#x27;, &amp;#x27;6d36bade-c33c-405e-88a8-3da6b1f8a1b8/p2g_Protein_chain_A.itp&amp;#x27;, &amp;#x27;6d36bade-c33c-405e-88a8-3da6b1f8a1b8/posre_Ion.itp&amp;#x27;, &amp;#x27;6d36bade-c33c-405e-88a8-3da6b1f8a1b8/posre_Protein_chain_A.itp&amp;#x27;]\n2024-11-04 14:30:12,745 [MainThread  ] [INFO ]  Unzipping: \n2024-11-04 14:30:12,745 [MainThread  ] [INFO ]  /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/mut_gmx.top.zip\n2024-11-04 14:30:12,745 [MainThread  ] [INFO ]  To: \n2024-11-04 14:30:12,745 [MainThread  ] [INFO ]  6d36bade-c33c-405e-88a8-3da6b1f8a1b8/p2g.top\n2024-11-04 14:30:12,746 [MainThread  ] [INFO ]  6d36bade-c33c-405e-88a8-3da6b1f8a1b8/p2g_Ion.itp\n2024-11-04 14:30:12,746 [MainThread  ] [INFO ]  6d36bade-c33c-405e-88a8-3da6b1f8a1b8/p2g_Protein_chain_A.itp\n2024-11-04 14:30:12,746 [MainThread  ] [INFO ]  6d36bade-c33c-405e-88a8-3da6b1f8a1b8/posre_Ion.itp\n2024-11-04 14:30:12,746 [MainThread  ] [INFO ]  6d36bade-c33c-405e-88a8-3da6b1f8a1b8/posre_Protein_chain_A.itp\n2024-11-04 14:30:12,746 [MainThread  ] [INFO ]  unique_dir_output_file: 70f10e30-147c-4a3f-96ec-49acf456d738/pmxgentop_p2g.top\n2024-11-04 14:30:12,746 [MainThread  ] [INFO ]  pmx gentop -o 70f10e30-147c-4a3f-96ec-49acf456d738/pmxgentop_p2g.top -ff amber99sb-star-ildn-mut -p 6d36bade-c33c-405e-88a8-3da6b1f8a1b8/p2g.top\n\n2024-11-04 14:30:19,891 [MainThread  ] [INFO ]  Executing: pmx gentop -o 70f10e30-147c-4a3f-96ec-49acf456d738/pmxgentop_p2g.top -ff amber99...\n2024-11-04 14:30:19,891 [MainThread  ] [INFO ]  Exit code: 0\n2024-11-04 14:30:19,891 [MainThread  ] [INFO ]  \nlog_&amp;gt; Reading input top file &amp;quot;6d36bade-c33c-405e-88a8-3da6b1f8a1b8/p2g.top&amp;quot;\nlog_&amp;gt; Making bonds for state B -&amp;gt; 0 bonds with perturbed atoms\nlog_&amp;gt; Making angles for state B -&amp;gt; 0 angles with perturbed atoms\nlog_&amp;gt; Making dihedrals for state B -&amp;gt; 0 dihedrals with perturbed atoms\nlog_&amp;gt; Removed 0 fake dihedrals\nlog_&amp;gt; Total charge of state A = 0\nlog_&amp;gt; Total charge of state B = 0\n\nlog_&amp;gt; Reading input itp file &amp;quot;p2g_Protein_chain_A.itp&amp;quot;&amp;quot;\nlog_&amp;gt; Scanning database for I2A \nlog_&amp;gt; Hybrid Residue -&amp;gt; 10 | I2A \nlog_&amp;gt; Making bonds for state B -&amp;gt; 22 bonds with perturbed atoms\nlog_&amp;gt; Making angles for state B -&amp;gt; 49 angles with perturbed atoms\nlog_&amp;gt; Making dihedrals for state B -&amp;gt; 57 dihedrals with perturbed atoms\nlog_&amp;gt; Removed 12 fake dihedrals\nlog_&amp;gt; Total charge of state A = 10\nlog_&amp;gt; Total charge of state B = 10\n\nlog_&amp;gt; Reading input itp file &amp;quot;p2g_Ion.itp&amp;quot;&amp;quot;\nlog_&amp;gt; Making bonds for state B -&amp;gt; 0 bonds with perturbed atoms\nlog_&amp;gt; Making angles for state B -&amp;gt; 0 angles with perturbed atoms\nlog_&amp;gt; Making dihedrals for state B -&amp;gt; 0 dihedrals with perturbed atoms\nlog_&amp;gt; Removed 0 fake dihedrals\nlog_&amp;gt; Total charge of state A = -10\nlog_&amp;gt; Total charge of state B = -10\n\nlog_&amp;gt; Writing itp file &amp;quot;/tmp/biobb/unitests_29/pmxgentop/70f10e30-147c-4a3f-96ec-49acf456d738/pmx_p2g_Protein_chain_A.itp&amp;quot;&amp;quot;\n\nlog_&amp;gt; Writing itp file &amp;quot;/tmp/biobb/unitests_29/pmxgentop/70f10e30-147c-4a3f-96ec-49acf456d738/pmx_p2g_Ion.itp&amp;quot;&amp;quot;\n\nlog_&amp;gt; Writing topology file &amp;quot;70f10e30-147c-4a3f-96ec-49acf456d738/pmxgentop_p2g.top&amp;quot;&amp;quot;\n\nb-states filled...........\n\n\n2024-11-04 14:30:19,892 [MainThread  ] [INFO ]  Check if 70f10e30-147c-4a3f-96ec-49acf456d738/p2g_Protein_chain_A.itp exists\n2024-11-04 14:30:19,893 [MainThread  ] [INFO ]  Copying 6d36bade-c33c-405e-88a8-3da6b1f8a1b8/p2g_Protein_chain_A.itp to: 70f10e30-147c-4a3f-96ec-49acf456d738\n2024-11-04 14:30:19,893 [MainThread  ] [INFO ]  Check if 70f10e30-147c-4a3f-96ec-49acf456d738/p2g_Ion.itp exists\n2024-11-04 14:30:19,893 [MainThread  ] [INFO ]  Copying 6d36bade-c33c-405e-88a8-3da6b1f8a1b8/p2g_Ion.itp to: 70f10e30-147c-4a3f-96ec-49acf456d738\n2024-11-04 14:30:19,893 [MainThread  ] [INFO ]  Check if 70f10e30-147c-4a3f-96ec-49acf456d738/p2g.top exists\n2024-11-04 14:30:19,894 [MainThread  ] [INFO ]  Copying 6d36bade-c33c-405e-88a8-3da6b1f8a1b8/p2g.top to: 70f10e30-147c-4a3f-96ec-49acf456d738\n2024-11-04 14:30:19,894 [MainThread  ] [INFO ]  Check if 70f10e30-147c-4a3f-96ec-49acf456d738/posre_Protein_chain_A.itp exists\n2024-11-04 14:30:19,894 [MainThread  ] [INFO ]  Copying 6d36bade-c33c-405e-88a8-3da6b1f8a1b8/posre_Protein_chain_A.itp to: 70f10e30-147c-4a3f-96ec-49acf456d738\n2024-11-04 14:30:19,894 [MainThread  ] [INFO ]  Check if 70f10e30-147c-4a3f-96ec-49acf456d738/posre_Ion.itp exists\n2024-11-04 14:30:19,894 [MainThread  ] [INFO ]  Copying 6d36bade-c33c-405e-88a8-3da6b1f8a1b8/posre_Ion.itp to: 70f10e30-147c-4a3f-96ec-49acf456d738\n2024-11-04 14:30:19,894 [MainThread  ] [INFO ]  Compressing topology to: /tmp/biobb/unitests_29/pmxgentop/output_topology.zip\n2024-11-04 14:30:19,895 [MainThread  ] [INFO ]  Ignored file 70f10e30-147c-4a3f-96ec-49acf456d738/amber99sb-star-ildn-mut.ff/forcefield.itp\n2024-11-04 14:30:19,910 [MainThread  ] [INFO ]  Ignored file 70f10e30-147c-4a3f-96ec-49acf456d738/amber99sb-star-ildn-mut.ff/spce.itp\n2024-11-04 14:30:19,910 [MainThread  ] [INFO ]  Ignored file 70f10e30-147c-4a3f-96ec-49acf456d738/amber99sb-star-ildn-mut.ff/ions.itp\n2024-11-04 14:30:19,913 [MainThread  ] [INFO ]  Adding:\n2024-11-04 14:30:19,913 [MainThread  ] [INFO ]  [&amp;#x27;70f10e30-147c-4a3f-96ec-49acf456d738/pmx_p2g_Ion.itp&amp;#x27;, &amp;#x27;70f10e30-147c-4a3f-96ec-49acf456d738/pmx_p2g_Protein_chain_A.itp&amp;#x27;, &amp;#x27;70f10e30-147c-4a3f-96ec-49acf456d738/pmxgentop_p2g.top&amp;#x27;, &amp;#x27;70f10e30-147c-4a3f-96ec-49acf456d738/posre_Ion.itp&amp;#x27;, &amp;#x27;70f10e30-147c-4a3f-96ec-49acf456d738/posre_Protein_chain_A.itp&amp;#x27;]\n2024-11-04 14:30:19,913 [MainThread  ] [INFO ]  to: /tmp/biobb/unitests_29/pmxgentop/output_topology.zip\n2024-11-04 14:30:19,949 [MainThread  ] [INFO ]  Removed: [&amp;#x27;70f10e30-147c-4a3f-96ec-49acf456d738/posre_Protein_chain_A.itp&amp;#x27;, &amp;#x27;70f10e30-147c-4a3f-96ec-49acf456d738/pmx_p2g_Protein_chain_A.itp&amp;#x27;, &amp;#x27;70f10e30-147c-4a3f-96ec-49acf456d738/posre_Ion.itp&amp;#x27;, &amp;#x27;70f10e30-147c-4a3f-96ec-49acf456d738/pmx_p2g_Ion.itp&amp;#x27;, &amp;#x27;70f10e30-147c-4a3f-96ec-49acf456d738/pmxgentop_p2g.top&amp;#x27;]\n2024-11-04 14:30:19,949 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_29/pmxgentop/output_topology.zip\nThis is a ZIP comparison!\nUnzipping:\nCreating a unique_dir for: /tmp/biobb/unitests_29/pmxgentop/output_topology.zip\nCreating a unique_dir for: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/reference/pmx/ref_mut_gmx_hybrid_top.zip\nComparing TOP/ITP:\n     FILE_A: 49515ad3-b806-4b8d-87f0-616a8de02db4/pmx_p2g_Ion.itp\n     FILE_B: 13b49bf5-97d9-4391-8b52-5f3d74687a3d/pmx_p2g_Ion.itp\nComparing TOP/ITP:\n     FILE_A: 49515ad3-b806-4b8d-87f0-616a8de02db4/pmx_p2g_Protein_chain_A.itp\n     FILE_B: 13b49bf5-97d9-4391-8b52-5f3d74687a3d/pmx_p2g_Protein_chain_A.itp\nComparing TOP/ITP:\n     FILE_A: 49515ad3-b806-4b8d-87f0-616a8de02db4/pmxgentop_p2g.top\n     FILE_B: 13b49bf5-97d9-4391-8b52-5f3d74687a3d/pmxgentop_p2g.top\nComparing TOP/ITP:\n     FILE_A: 49515ad3-b806-4b8d-87f0-616a8de02db4/posre_Ion.itp\n     FILE_B: 13b49bf5-97d9-4391-8b52-5f3d74687a3d/posre_Ion.itp\nComparing TOP/ITP:\n     FILE_A: 49515ad3-b806-4b8d-87f0-616a8de02db4/posre_Protein_chain_A.itp\n     FILE_B: 13b49bf5-97d9-4391-8b52-5f3d74687a3d/posre_Protein_chain_A.itp\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_29/pmxgentop/pmxgentop_log.out:file_utils.py:409 Module: biobb_pmx.pmxbiobb.pmxgentop Version: 4.2.1\nINFO     /tmp/biobb/unitests_29/pmxgentop/pmxgentop_log.out:file_utils.py:82 /tmp/biobb/unitests_29/pmxgentop/sandbox_44db0fd9-cd06-4ac0-90db-66fc666d9b2e directory successfully created\nINFO     /tmp/biobb/unitests_29/pmxgentop/pmxgentop_log.out:file_utils.py:172 Extracting: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/mut_gmx.top.zip\nINFO     /tmp/biobb/unitests_29/pmxgentop/pmxgentop_log.out:file_utils.py:173 to:\nINFO     /tmp/biobb/unitests_29/pmxgentop/pmxgentop_log.out:file_utils.py:174 [&amp;#x27;6d36bade-c33c-405e-88a8-3da6b1f8a1b8/p2g.top&amp;#x27;, &amp;#x27;6d36bade-c33c-405e-88a8-3da6b1f8a1b8/p2g_Ion.itp&amp;#x27;, &amp;#x27;6d36bade-c33c-405e-88a8-3da6b1f8a1b8/p2g_Protein_chain_A.itp&amp;#x27;, &amp;#x27;6d36bade-c33c-405e-88a8-3da6b1f8a1b8/posre_Ion.itp&amp;#x27;, &amp;#x27;6d36bade-c33c-405e-88a8-3da6b1f8a1b8/posre_Protein_chain_A.itp&amp;#x27;]\nINFO     /tmp/biobb/unitests_29/pmxgentop/pmxgentop_log.out:file_utils.py:252 Unzipping: \nINFO     /tmp/biobb/unitests_29/pmxgentop/pmxgentop_log.out:file_utils.py:253 /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/mut_gmx.top.zip\nINFO     /tmp/biobb/unitests_29/pmxgentop/pmxgentop_log.out:file_utils.py:254 To: \nINFO     /tmp/biobb/unitests_29/pmxgentop/pmxgentop_log.out:file_utils.py:256 6d36bade-c33c-405e-88a8-3da6b1f8a1b8/p2g.top\nINFO     /tmp/biobb/unitests_29/pmxgentop/pmxgentop_log.out:file_utils.py:256 6d36bade-c33c-405e-88a8-3da6b1f8a1b8/p2g_Ion.itp\nINFO     /tmp/biobb/unitests_29/pmxgentop/pmxgentop_log.out:file_utils.py:256 6d36bade-c33c-405e-88a8-3da6b1f8a1b8/p2g_Protein_chain_A.itp\nINFO     /tmp/biobb/unitests_29/pmxgentop/pmxgentop_log.out:file_utils.py:256 6d36bade-c33c-405e-88a8-3da6b1f8a1b8/posre_Ion.itp\nINFO     /tmp/biobb/unitests_29/pmxgentop/pmxgentop_log.out:file_utils.py:256 6d36bade-c33c-405e-88a8-3da6b1f8a1b8/posre_Protein_chain_A.itp\nINFO     /tmp/biobb/unitests_29/pmxgentop/pmxgentop_log.out:file_utils.py:409 unique_dir_output_file: 70f10e30-147c-4a3f-96ec-49acf456d738/pmxgentop_p2g.top\nINFO     /tmp/biobb/unitests_29/pmxgentop/pmxgentop_log.out:cmd_wrapper.py:63 pmx gentop -o 70f10e30-147c-4a3f-96ec-49acf456d738/pmxgentop_p2g.top -ff amber99sb-star-ildn-mut -p 6d36bade-c33c-405e-88a8-3da6b1f8a1b8/p2g.top\n\nINFO     /tmp/biobb/unitests_29/pmxgentop/pmxgentop_log.out:cmd_wrapper.py:36 Executing: pmx gentop -o 70f10e30-147c-4a3f-96ec-49acf456d738/pmxgentop_p2g.top -ff amber99...\nINFO     /tmp/biobb/unitests_29/pmxgentop/pmxgentop_log.out:cmd_wrapper.py:37 Exit code: 0\nINFO     /tmp/biobb/unitests_29/pmxgentop/pmxgentop_log.out:cmd_wrapper.py:41 \nlog_&amp;gt; Reading input top file &amp;quot;6d36bade-c33c-405e-88a8-3da6b1f8a1b8/p2g.top&amp;quot;\nlog_&amp;gt; Making bonds for state B -&amp;gt; 0 bonds with perturbed atoms\nlog_&amp;gt; Making angles for state B -&amp;gt; 0 angles with perturbed atoms\nlog_&amp;gt; Making dihedrals for state B -&amp;gt; 0 dihedrals with perturbed atoms\nlog_&amp;gt; Removed 0 fake dihedrals\nlog_&amp;gt; Total charge of state A = 0\nlog_&amp;gt; Total charge of state B = 0\n\nlog_&amp;gt; Reading input itp file &amp;quot;p2g_Protein_chain_A.itp&amp;quot;&amp;quot;\nlog_&amp;gt; Scanning database for I2A \nlog_&amp;gt; Hybrid Residue -&amp;gt; 10 | I2A \nlog_&amp;gt; Making bonds for state B -&amp;gt; 22 bonds with perturbed atoms\nlog_&amp;gt; Making angles for state B -&amp;gt; 49 angles with perturbed atoms\nlog_&amp;gt; Making dihedrals for state B -&amp;gt; 57 dihedrals with perturbed atoms\nlog_&amp;gt; Removed 12 fake dihedrals\nlog_&amp;gt; Total charge of state A = 10\nlog_&amp;gt; Total charge of state B = 10\n\nlog_&amp;gt; Reading input itp file &amp;quot;p2g_Ion.itp&amp;quot;&amp;quot;\nlog_&amp;gt; Making bonds for state B -&amp;gt; 0 bonds with perturbed atoms\nlog_&amp;gt; Making angles for state B -&amp;gt; 0 angles with perturbed atoms\nlog_&amp;gt; Making dihedrals for state B -&amp;gt; 0 dihedrals with perturbed atoms\nlog_&amp;gt; Removed 0 fake dihedrals\nlog_&amp;gt; Total charge of state A = -10\nlog_&amp;gt; Total charge of state B = -10\n\nlog_&amp;gt; Writing itp file &amp;quot;/tmp/biobb/unitests_29/pmxgentop/70f10e30-147c-4a3f-96ec-49acf456d738/pmx_p2g_Protein_chain_A.itp&amp;quot;&amp;quot;\n\nlog_&amp;gt; Writing itp file &amp;quot;/tmp/biobb/unitests_29/pmxgentop/70f10e30-147c-4a3f-96ec-49acf456d738/pmx_p2g_Ion.itp&amp;quot;&amp;quot;\n\nlog_&amp;gt; Writing topology file &amp;quot;70f10e30-147c-4a3f-96ec-49acf456d738/pmxgentop_p2g.top&amp;quot;&amp;quot;\n\nb-states filled...........\n\n\nINFO     /tmp/biobb/unitests_29/pmxgentop/pmxgentop_log.out:file_utils.py:409 Check if 70f10e30-147c-4a3f-96ec-49acf456d738/p2g_Protein_chain_A.itp exists\nINFO     /tmp/biobb/unitests_29/pmxgentop/pmxgentop_log.out:file_utils.py:409 Copying 6d36bade-c33c-405e-88a8-3da6b1f8a1b8/p2g_Protein_chain_A.itp to: 70f10e30-147c-4a3f-96ec-49acf456d738\nINFO     /tmp/biobb/unitests_29/pmxgentop/pmxgentop_log.out:file_utils.py:409 Check if 70f10e30-147c-4a3f-96ec-49acf456d738/p2g_Ion.itp exists\nINFO     /tmp/biobb/unitests_29/pmxgentop/pmxgentop_log.out:file_utils.py:409 Copying 6d36bade-c33c-405e-88a8-3da6b1f8a1b8/p2g_Ion.itp to: 70f10e30-147c-4a3f-96ec-49acf456d738\nINFO     /tmp/biobb/unitests_29/pmxgentop/pmxgentop_log.out:file_utils.py:409 Check if 70f10e30-147c-4a3f-96ec-49acf456d738/p2g.top exists\nINFO     /tmp/biobb/unitests_29/pmxgentop/pmxgentop_log.out:file_utils.py:409 Copying 6d36bade-c33c-405e-88a8-3da6b1f8a1b8/p2g.top to: 70f10e30-147c-4a3f-96ec-49acf456d738\nINFO     /tmp/biobb/unitests_29/pmxgentop/pmxgentop_log.out:file_utils.py:409 Check if 70f10e30-147c-4a3f-96ec-49acf456d738/posre_Protein_chain_A.itp exists\nINFO     /tmp/biobb/unitests_29/pmxgentop/pmxgentop_log.out:file_utils.py:409 Copying 6d36bade-c33c-405e-88a8-3da6b1f8a1b8/posre_Protein_chain_A.itp to: 70f10e30-147c-4a3f-96ec-49acf456d738\nINFO     /tmp/biobb/unitests_29/pmxgentop/pmxgentop_log.out:file_utils.py:409 Check if 70f10e30-147c-4a3f-96ec-49acf456d738/posre_Ion.itp exists\nINFO     /tmp/biobb/unitests_29/pmxgentop/pmxgentop_log.out:file_utils.py:409 Copying 6d36bade-c33c-405e-88a8-3da6b1f8a1b8/posre_Ion.itp to: 70f10e30-147c-4a3f-96ec-49acf456d738\nINFO     /tmp/biobb/unitests_29/pmxgentop/pmxgentop_log.out:file_utils.py:409 Compressing topology to: /tmp/biobb/unitests_29/pmxgentop/output_topology.zip\nINFO     /tmp/biobb/unitests_29/pmxgentop/pmxgentop_log.out:file_utils.py:203 Ignored file 70f10e30-147c-4a3f-96ec-49acf456d738/amber99sb-star-ildn-mut.ff/forcefield.itp\nINFO     /tmp/biobb/unitests_29/pmxgentop/pmxgentop_log.out:file_utils.py:203 Ignored file 70f10e30-147c-4a3f-96ec-49acf456d738/amber99sb-star-ildn-mut.ff/spce.itp\nINFO     /tmp/biobb/unitests_29/pmxgentop/pmxgentop_log.out:file_utils.py:203 Ignored file 70f10e30-147c-4a3f-96ec-49acf456d738/amber99sb-star-ildn-mut.ff/ions.itp\nINFO     /tmp/biobb/unitests_29/pmxgentop/pmxgentop_log.out:file_utils.py:148 Adding:\nINFO     /tmp/biobb/unitests_29/pmxgentop/pmxgentop_log.out:file_utils.py:149 [&amp;#x27;70f10e30-147c-4a3f-96ec-49acf456d738/pmx_p2g_Ion.itp&amp;#x27;, &amp;#x27;70f10e30-147c-4a3f-96ec-49acf456d738/pmx_p2g_Protein_chain_A.itp&amp;#x27;, &amp;#x27;70f10e30-147c-4a3f-96ec-49acf456d738/pmxgentop_p2g.top&amp;#x27;, &amp;#x27;70f10e30-147c-4a3f-96ec-49acf456d738/posre_Ion.itp&amp;#x27;, &amp;#x27;70f10e30-147c-4a3f-96ec-49acf456d738/posre_Protein_chain_A.itp&amp;#x27;]\nINFO     /tmp/biobb/unitests_29/pmxgentop/pmxgentop_log.out:file_utils.py:150 to: /tmp/biobb/unitests_29/pmxgentop/output_topology.zip\nINFO     /tmp/biobb/unitests_29/pmxgentop/pmxgentop_log.out:file_utils.py:409 Removed: [&amp;#x27;70f10e30-147c-4a3f-96ec-49acf456d738/posre_Protein_chain_A.itp&amp;#x27;, &amp;#x27;70f10e30-147c-4a3f-96ec-49acf456d738/pmx_p2g_Protein_chain_A.itp&amp;#x27;, &amp;#x27;70f10e30-147c-4a3f-96ec-49acf456d738/posre_Ion.itp&amp;#x27;, &amp;#x27;70f10e30-147c-4a3f-96ec-49acf456d738/pmx_p2g_Ion.itp&amp;#x27;, &amp;#x27;70f10e30-147c-4a3f-96ec-49acf456d738/pmxgentop_p2g.top&amp;#x27;]\nINFO     /tmp/biobb/unitests_29/pmxgentop/pmxgentop_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_29\n&#34;}], &#34;biobb_pmx/test/unitests/test_pmx/test_pmxligand_hybrid.py::TestPmxligand_hybrid::test_pmxligand_hybrid&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_pmx/test/unitests/test_pmx/test_pmxligand_hybrid.py::TestPmxligand_hybrid::test_pmxligand_hybrid&#34;, &#34;duration&#34;: &#34;00:00:02&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_pmx/test/unitests/test_pmx/test_pmxligand_hybrid.py::TestPmxligand_hybrid::test_pmxligand_hybrid&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:00:02&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-11-04 14:30:20,161 [MainThread  ] [INFO ]  Module: biobb_pmx.pmxbiobb.pmxligand_hybrid Version: 4.2.1\n2024-11-04 14:30:20,162 [MainThread  ] [INFO ]  /tmp/biobb/unitests_29/pmxligand_hybrid/sandbox_e8f90aaa-e96b-4458-9806-251ef62c4e19 directory successfully created\n2024-11-04 14:30:20,162 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/lig1.pdb to /tmp/biobb/unitests_29/pmxligand_hybrid/sandbox_e8f90aaa-e96b-4458-9806-251ef62c4e19\n2024-11-04 14:30:20,162 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/lig2.pdb to /tmp/biobb/unitests_29/pmxligand_hybrid/sandbox_e8f90aaa-e96b-4458-9806-251ef62c4e19\n2024-11-04 14:30:20,162 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/topoLig1.itp to /tmp/biobb/unitests_29/pmxligand_hybrid/sandbox_e8f90aaa-e96b-4458-9806-251ef62c4e19\n2024-11-04 14:30:20,163 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/topoLig2.itp to /tmp/biobb/unitests_29/pmxligand_hybrid/sandbox_e8f90aaa-e96b-4458-9806-251ef62c4e19\n2024-11-04 14:30:20,163 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/myPairs1.dat to /tmp/biobb/unitests_29/pmxligand_hybrid/sandbox_e8f90aaa-e96b-4458-9806-251ef62c4e19\n2024-11-04 14:30:20,163 [MainThread  ] [INFO ]  pmx ligandHybrid -i1 /tmp/biobb/unitests_29/pmxligand_hybrid/sandbox_e8f90aaa-e96b-4458-9806-251ef62c4e19/lig1.pdb -i2 /tmp/biobb/unitests_29/pmxligand_hybrid/sandbox_e8f90aaa-e96b-4458-9806-251ef62c4e19/lig2.pdb -itp1 /tmp/biobb/unitests_29/pmxligand_hybrid/sandbox_e8f90aaa-e96b-4458-9806-251ef62c4e19/topoLig1.itp -itp2 /tmp/biobb/unitests_29/pmxligand_hybrid/sandbox_e8f90aaa-e96b-4458-9806-251ef62c4e19/topoLig2.itp -pairs /tmp/biobb/unitests_29/pmxligand_hybrid/sandbox_e8f90aaa-e96b-4458-9806-251ef62c4e19/myPairs1.dat -oA /tmp/biobb/unitests_29/pmxligand_hybrid/sandbox_e8f90aaa-e96b-4458-9806-251ef62c4e19/hybridStruct1.pdb -oB /tmp/biobb/unitests_29/pmxligand_hybrid/sandbox_e8f90aaa-e96b-4458-9806-251ef62c4e19/hybridStruct2.pdb -oitp /tmp/biobb/unitests_29/pmxligand_hybrid/sandbox_e8f90aaa-e96b-4458-9806-251ef62c4e19/hybridTopo.itp -offitp /tmp/biobb/unitests_29/pmxligand_hybrid/sandbox_e8f90aaa-e96b-4458-9806-251ef62c4e19/hybridAtomTypes.itp -log /tmp/biobb/unitests_29/pmxligand_hybrid/sandbox_e8f90aaa-e96b-4458-9806-251ef62c4e19/ligand_hybrid.log --fit --d 0.05\n\n2024-11-04 14:30:21,866 [MainThread  ] [INFO ]  Executing: pmx ligandHybrid -i1 /tmp/biobb/unitests_29/pmxligand_hybrid/sandbox_e8f90aaa-e9...\n2024-11-04 14:30:21,866 [MainThread  ] [INFO ]  Exit code: 0\n2024-11-04 14:30:21,867 [MainThread  ] [INFO ]  ligandHybridTop__log_&amp;gt; Reading ligand 1 from: &amp;quot;/tmp/biobb/unitests_29/pmxligand_hybrid/sandbox_e8f90aaa-e96b-4458-9806-251ef62c4e19/lig1.pdb&amp;quot;\nligandHybridTop__log_&amp;gt; Reading ligand 2 from: &amp;quot;/tmp/biobb/unitests_29/pmxligand_hybrid/sandbox_e8f90aaa-e96b-4458-9806-251ef62c4e19/lig2.pdb&amp;quot;\nligandHybridTop__log_&amp;gt; Reading topology 1 from: &amp;quot;/tmp/biobb/unitests_29/pmxligand_hybrid/sandbox_e8f90aaa-e96b-4458-9806-251ef62c4e19/topoLig1.itp&amp;quot;\nligandHybridTop__log_&amp;gt; Reading topology 2 from: &amp;quot;/tmp/biobb/unitests_29/pmxligand_hybrid/sandbox_e8f90aaa-e96b-4458-9806-251ef62c4e19/topoLig2.itp&amp;quot;\nligandHybridTop__log_&amp;gt; Reading file with atom pairs: &amp;quot;/tmp/biobb/unitests_29/pmxligand_hybrid/sandbox_e8f90aaa-e96b-4458-9806-251ef62c4e19/myPairs1.dat&amp;quot;\nligandHybridTop__log_&amp;gt; Assigning forcefield parameters....\nligandHybridTop__log_&amp;gt; Superimposing mol2 on mol1\nligandHybridTop__log_&amp;gt; Superimposing mol1 on mol2\nligandHybridTop__log_&amp;gt; Initializing the main object for LigandHybridTopology\nligandHybridTop__log_&amp;gt; Starting hybrid topology generation\nligandHybridTop__log_&amp;gt; Making atom pairs.....\nligandHybridTop__log_&amp;gt; Identifying dummies.....\nligandHybridTop__log_&amp;gt; Generated 33 atom-atom pairs\nligandHybridTop__log_&amp;gt; Dummies in state A: 6\nligandHybridTop__log_&amp;gt; Dummies in state B: 6\nligandHybridTop__log_&amp;gt; Making B-states....\nligandHybridTop__log_&amp;gt; Atom....:    2            c3 |   0.14 |  12.01 -&amp;gt;           c3 |   0.14 |  12.01\nligandHybridTop__log_&amp;gt; Atom....:   27            h1 |   0.05 |   1.01 -&amp;gt;           h1 |   0.05 |   1.01\nligandHybridTop__log_&amp;gt; Atom....:   28            h1 |   0.05 |   1.01 -&amp;gt;           h1 |   0.05 |   1.01\nligandHybridTop__log_&amp;gt; Atom....:    1            c3 |  -0.11 |  12.01 -&amp;gt;           c3 |  -0.11 |  12.01\nligandHybridTop__log_&amp;gt; Atom....:   24            hc |   0.05 |   1.01 -&amp;gt;           hc |   0.05 |   1.01\nligandHybridTop__log_&amp;gt; Atom....:   25            hc |   0.05 |   1.01 -&amp;gt;           hc |   0.05 |   1.01\nligandHybridTop__log_&amp;gt; Atom....:   26            hc |   0.05 |   1.01 -&amp;gt;           hc |   0.05 |   1.01\nligandHybridTop__log_&amp;gt; Atom....:    3            os |  -0.44 |  16.00 -&amp;gt;           os |  -0.44 |  16.00\nligandHybridTop__log_&amp;gt; Atom....:    4            ca |   0.74 |  12.01 -&amp;gt;           ca |   0.74 |  12.01\nligandHybridTop__log_&amp;gt; Atom....:    5            nb |  -0.83 |  14.01 -&amp;gt;           nb |  -0.83 |  14.01\nligandHybridTop__log_&amp;gt; Atom....:    6            ca |   0.63 |  12.01 -&amp;gt;           ca |   0.62 |  12.01\nligandHybridTop__log_&amp;gt; Atom....:    7            ca |  -0.39 |  12.01 -&amp;gt;           ca |  -0.39 |  12.01\nligandHybridTop__log_&amp;gt; Atom....:   29            ha |   0.18 |   1.01 -&amp;gt;           ha |   0.18 |   1.01\nligandHybridTop__log_&amp;gt; Atom....:    8            ca |   0.31 |  12.01 -&amp;gt;           ca |   0.31 |  12.01\nligandHybridTop__log_&amp;gt; Atom....:   10            ca |  -0.28 |  12.01 -&amp;gt;           ca |  -0.28 |  12.01\nligandHybridTop__log_&amp;gt; Atom....:   11            cg |   0.27 |  12.01 -&amp;gt;           cg |   0.27 |  12.01\nligandHybridTop__log_&amp;gt; Atom....:   12            n1 |  -0.39 |  14.01 -&amp;gt;           n1 |  -0.39 |  14.01\nligandHybridTop__log_&amp;gt; Atom....:    9            nv |  -0.86 |  14.01 -&amp;gt;           nv |  -0.86 |  14.01\nligandHybridTop__log_&amp;gt; Atom....:   13            ns |  -0.55 |  14.01 -&amp;gt;           ns |  -0.55 |  14.01\nligandHybridTop__log_&amp;gt; Atom....:   14             c |   0.68 |  12.01 -&amp;gt;            c |   0.67 |  12.01\nligandHybridTop__log_&amp;gt; Atom....:   15             o |  -0.58 |  16.00 -&amp;gt;            o |  -0.58 |  16.00\nligandHybridTop__log_&amp;gt; Atom....:   16            c3 |  -0.11 |  12.01 -&amp;gt;           c3 |  -0.11 |  12.01\nligandHybridTop__log_&amp;gt; Atom....:   33            hc |   0.09 |   1.01 -&amp;gt;           hc |   0.09 |   1.01\nligandHybridTop__log_&amp;gt; Atom....:   34            hc |   0.09 |   1.01 -&amp;gt;           hc |   0.09 |   1.01\nligandHybridTop__log_&amp;gt; Atom....:   17            ca |  -0.10 |  12.01 -&amp;gt;           ca |  -0.09 |  12.01\nligandHybridTop__log_&amp;gt; Atom....:   18            ca |   0.03 |  12.01 -&amp;gt;           ca |  -0.11 |  12.01\nligandHybridTop__log_&amp;gt; Atom....:   20            ca |  -0.12 |  12.01 -&amp;gt;           ca |   0.02 |  12.01\nligandHybridTop__log_&amp;gt; Atom....:   21            ca |  -0.11 |  12.01 -&amp;gt;           ca |  -0.12 |  12.01\nligandHybridTop__log_&amp;gt; Atom....:   36            ha |   0.14 |   1.01 -&amp;gt;           ha |   0.15 |   1.01\nligandHybridTop__log_&amp;gt; Atom....:   22            ca |  -0.12 |  12.01 -&amp;gt;           ca |  -0.12 |  12.01\nligandHybridTop__log_&amp;gt; Atom....:   37            ha |   0.14 |   1.01 -&amp;gt;           ha |   0.14 |   1.01\nligandHybridTop__log_&amp;gt; Atom....:   23            ca |  -0.12 |  12.01 -&amp;gt;           ca |  -0.13 |  12.01\nligandHybridTop__log_&amp;gt; Atom....:   38            ha |   0.14 |   1.01 -&amp;gt;           ha |   0.14 |   1.01\nligandHybridTop__log_&amp;gt; Constructing dummies....\nligandHybridTop__log_&amp;gt; Dummies in stateA: \nligandHybridTop__log_&amp;gt; Dummy...:   40        DUM_cl |   0.00 |  35.45 -&amp;gt;           cl |  -0.12 |  35.45\nligandHybridTop__log_&amp;gt; Dummy...:   41        DUM_hn |   0.00 |   1.01 -&amp;gt;           hn |   0.44 |   1.01\nligandHybridTop__log_&amp;gt; Dummy...:   42        DUM_hn |   0.00 |   1.01 -&amp;gt;           hn |   0.44 |   1.01\nligandHybridTop__log_&amp;gt; Dummy...:   43        DUM_hn |   0.00 |   1.01 -&amp;gt;           hn |   0.34 |   1.01\nligandHybridTop__log_&amp;gt; Dummy...:   44        DUM_ha |   0.00 |   1.01 -&amp;gt;           ha |   0.16 |   1.01\nligandHybridTop__log_&amp;gt; Dummy...:   45        DUM_DU |   0.00 |   0.00 -&amp;gt;           DU |   0.04 |   0.00\nligandHybridTop__log_&amp;gt; Dummies in stateB: \nligandHybridTop__log_&amp;gt; Dummy...:   19            cl |  -0.11 |  35.45 -&amp;gt;       DUM_cl |   0.00 |  35.45\nligandHybridTop__log_&amp;gt; Dummy...:   30            hn |   0.44 |   1.01 -&amp;gt;       DUM_hn |   0.00 |   1.01\nligandHybridTop__log_&amp;gt; Dummy...:   31            hn |   0.44 |   1.01 -&amp;gt;       DUM_hn |   0.00 |   1.01\nligandHybridTop__log_&amp;gt; Dummy...:   32            hn |   0.34 |   1.01 -&amp;gt;       DUM_hn |   0.00 |   1.01\nligandHybridTop__log_&amp;gt; Dummy...:   35            ha |   0.15 |   1.01 -&amp;gt;       DUM_ha |   0.00 |   1.01\nligandHybridTop__log_&amp;gt; Dummy...:   39            DU |   0.04 |   0.00 -&amp;gt;       DUM_DU |   0.00 |   0.00\nligandHybridTop__log_&amp;gt; Construct bonds....\nligandHybridTop__log_&amp;gt; Construct angles....\nligandHybridTop__log_&amp;gt; Construct dihedrals....\nligandHybridTop__log_&amp;gt; Construct vsites2....\nligandHybridTop__log_&amp;gt; Construct vsites3....\nligandHybridTop__log_&amp;gt; Construct exclusions....\nligandHybridTop__log_&amp;gt; Construct pairs (1-4 interactions)....\nligandHybridTop__log_&amp;gt; Assembling new itp....\nligandHybridTop__log_&amp;gt; Writing new itp file: &amp;quot;/tmp/biobb/unitests_29/pmxligand_hybrid/sandbox_e8f90aaa-e96b-4458-9806-251ef62c4e19/hybridTopo.itp&amp;quot;\nligandHybridTop__log_&amp;gt; Writing dummy forcefield file: &amp;quot;/tmp/biobb/unitests_29/pmxligand_hybrid/sandbox_e8f90aaa-e96b-4458-9806-251ef62c4e19/hybridAtomTypes.itp&amp;quot;\n\n2024-11-04 14:30:21,868 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_29/pmxligand_hybrid/sandbox_e8f90aaa-e96b-4458-9806-251ef62c4e19&amp;#x27;]\n2024-11-04 14:30:21,868 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_29/pmxligand_hybrid/hybridStruct1.pdb\nChecking if empty file: /tmp/biobb/unitests_29/pmxligand_hybrid/hybridStruct2.pdb\nChecking if empty file: /tmp/biobb/unitests_29/pmxligand_hybrid/hybridTopo.itp\nChecking if empty file: /tmp/biobb/unitests_29/pmxligand_hybrid/hybridAtomTypes.itp\nChecking RMSD between:\n     PDB_A: /tmp/biobb/unitests_29/pmxligand_hybrid/hybridStruct1.pdb\n     PDB_B: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/reference/pmx/ref_hybridStructure1.pdb\n     Ignoring HETAMT in RMSD\n     Ignoring Hydrogen atoms in RMSD\n     Atoms ALIGNED in PDB_A: 26\n     Atoms ALIGNED in PDB_B: 26\n     RMS: 3.850114164176677e-15\n     RMS_CUTOFF: 1\nChecking RMSD between:\n     PDB_A: /tmp/biobb/unitests_29/pmxligand_hybrid/hybridStruct2.pdb\n     PDB_B: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/reference/pmx/ref_hybridStructure2.pdb\n     Ignoring HETAMT in RMSD\n     Ignoring Hydrogen atoms in RMSD\n     Atoms ALIGNED in PDB_A: 26\n     Atoms ALIGNED in PDB_B: 26\n     RMS: 0.1872943529544109\n     RMS_CUTOFF: 1\nComparing TOP/ITP:\n     FILE_A: /tmp/biobb/unitests_29/pmxligand_hybrid/hybridTopo.itp\n     FILE_B: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/reference/pmx/ref_hybridTopology.itp\nComparing TOP/ITP:\n     FILE_A: /tmp/biobb/unitests_29/pmxligand_hybrid/hybridAtomTypes.itp\n     FILE_B: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/reference/pmx/ref_hybridAtomTypes.itp\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_29/pmxligand_hybrid/pmxligand_hybrid_log.out:file_utils.py:409 Module: biobb_pmx.pmxbiobb.pmxligand_hybrid Version: 4.2.1\nINFO     /tmp/biobb/unitests_29/pmxligand_hybrid/pmxligand_hybrid_log.out:file_utils.py:82 /tmp/biobb/unitests_29/pmxligand_hybrid/sandbox_e8f90aaa-e96b-4458-9806-251ef62c4e19 directory successfully created\nINFO     /tmp/biobb/unitests_29/pmxligand_hybrid/pmxligand_hybrid_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/lig1.pdb to /tmp/biobb/unitests_29/pmxligand_hybrid/sandbox_e8f90aaa-e96b-4458-9806-251ef62c4e19\nINFO     /tmp/biobb/unitests_29/pmxligand_hybrid/pmxligand_hybrid_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/lig2.pdb to /tmp/biobb/unitests_29/pmxligand_hybrid/sandbox_e8f90aaa-e96b-4458-9806-251ef62c4e19\nINFO     /tmp/biobb/unitests_29/pmxligand_hybrid/pmxligand_hybrid_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/topoLig1.itp to /tmp/biobb/unitests_29/pmxligand_hybrid/sandbox_e8f90aaa-e96b-4458-9806-251ef62c4e19\nINFO     /tmp/biobb/unitests_29/pmxligand_hybrid/pmxligand_hybrid_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/topoLig2.itp to /tmp/biobb/unitests_29/pmxligand_hybrid/sandbox_e8f90aaa-e96b-4458-9806-251ef62c4e19\nINFO     /tmp/biobb/unitests_29/pmxligand_hybrid/pmxligand_hybrid_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/myPairs1.dat to /tmp/biobb/unitests_29/pmxligand_hybrid/sandbox_e8f90aaa-e96b-4458-9806-251ef62c4e19\nINFO     /tmp/biobb/unitests_29/pmxligand_hybrid/pmxligand_hybrid_log.out:cmd_wrapper.py:63 pmx ligandHybrid -i1 /tmp/biobb/unitests_29/pmxligand_hybrid/sandbox_e8f90aaa-e96b-4458-9806-251ef62c4e19/lig1.pdb -i2 /tmp/biobb/unitests_29/pmxligand_hybrid/sandbox_e8f90aaa-e96b-4458-9806-251ef62c4e19/lig2.pdb -itp1 /tmp/biobb/unitests_29/pmxligand_hybrid/sandbox_e8f90aaa-e96b-4458-9806-251ef62c4e19/topoLig1.itp -itp2 /tmp/biobb/unitests_29/pmxligand_hybrid/sandbox_e8f90aaa-e96b-4458-9806-251ef62c4e19/topoLig2.itp -pairs /tmp/biobb/unitests_29/pmxligand_hybrid/sandbox_e8f90aaa-e96b-4458-9806-251ef62c4e19/myPairs1.dat -oA /tmp/biobb/unitests_29/pmxligand_hybrid/sandbox_e8f90aaa-e96b-4458-9806-251ef62c4e19/hybridStruct1.pdb -oB /tmp/biobb/unitests_29/pmxligand_hybrid/sandbox_e8f90aaa-e96b-4458-9806-251ef62c4e19/hybridStruct2.pdb -oitp /tmp/biobb/unitests_29/pmxligand_hybrid/sandbox_e8f90aaa-e96b-4458-9806-251ef62c4e19/hybridTopo.itp -offitp /tmp/biobb/unitests_29/pmxligand_hybrid/sandbox_e8f90aaa-e96b-4458-9806-251ef62c4e19/hybridAtomTypes.itp -log /tmp/biobb/unitests_29/pmxligand_hybrid/sandbox_e8f90aaa-e96b-4458-9806-251ef62c4e19/ligand_hybrid.log --fit --d 0.05\n\nINFO     /tmp/biobb/unitests_29/pmxligand_hybrid/pmxligand_hybrid_log.out:cmd_wrapper.py:36 Executing: pmx ligandHybrid -i1 /tmp/biobb/unitests_29/pmxligand_hybrid/sandbox_e8f90aaa-e9...\nINFO     /tmp/biobb/unitests_29/pmxligand_hybrid/pmxligand_hybrid_log.out:cmd_wrapper.py:37 Exit code: 0\nINFO     /tmp/biobb/unitests_29/pmxligand_hybrid/pmxligand_hybrid_log.out:cmd_wrapper.py:41 ligandHybridTop__log_&amp;gt; Reading ligand 1 from: &amp;quot;/tmp/biobb/unitests_29/pmxligand_hybrid/sandbox_e8f90aaa-e96b-4458-9806-251ef62c4e19/lig1.pdb&amp;quot;\nligandHybridTop__log_&amp;gt; Reading ligand 2 from: &amp;quot;/tmp/biobb/unitests_29/pmxligand_hybrid/sandbox_e8f90aaa-e96b-4458-9806-251ef62c4e19/lig2.pdb&amp;quot;\nligandHybridTop__log_&amp;gt; Reading topology 1 from: &amp;quot;/tmp/biobb/unitests_29/pmxligand_hybrid/sandbox_e8f90aaa-e96b-4458-9806-251ef62c4e19/topoLig1.itp&amp;quot;\nligandHybridTop__log_&amp;gt; Reading topology 2 from: &amp;quot;/tmp/biobb/unitests_29/pmxligand_hybrid/sandbox_e8f90aaa-e96b-4458-9806-251ef62c4e19/topoLig2.itp&amp;quot;\nligandHybridTop__log_&amp;gt; Reading file with atom pairs: &amp;quot;/tmp/biobb/unitests_29/pmxligand_hybrid/sandbox_e8f90aaa-e96b-4458-9806-251ef62c4e19/myPairs1.dat&amp;quot;\nligandHybridTop__log_&amp;gt; Assigning forcefield parameters....\nligandHybridTop__log_&amp;gt; Superimposing mol2 on mol1\nligandHybridTop__log_&amp;gt; Superimposing mol1 on mol2\nligandHybridTop__log_&amp;gt; Initializing the main object for LigandHybridTopology\nligandHybridTop__log_&amp;gt; Starting hybrid topology generation\nligandHybridTop__log_&amp;gt; Making atom pairs.....\nligandHybridTop__log_&amp;gt; Identifying dummies.....\nligandHybridTop__log_&amp;gt; Generated 33 atom-atom pairs\nligandHybridTop__log_&amp;gt; Dummies in state A: 6\nligandHybridTop__log_&amp;gt; Dummies in state B: 6\nligandHybridTop__log_&amp;gt; Making B-states....\nligandHybridTop__log_&amp;gt; Atom....:    2            c3 |   0.14 |  12.01 -&amp;gt;           c3 |   0.14 |  12.01\nligandHybridTop__log_&amp;gt; Atom....:   27            h1 |   0.05 |   1.01 -&amp;gt;           h1 |   0.05 |   1.01\nligandHybridTop__log_&amp;gt; Atom....:   28            h1 |   0.05 |   1.01 -&amp;gt;           h1 |   0.05 |   1.01\nligandHybridTop__log_&amp;gt; Atom....:    1            c3 |  -0.11 |  12.01 -&amp;gt;           c3 |  -0.11 |  12.01\nligandHybridTop__log_&amp;gt; Atom....:   24            hc |   0.05 |   1.01 -&amp;gt;           hc |   0.05 |   1.01\nligandHybridTop__log_&amp;gt; Atom....:   25            hc |   0.05 |   1.01 -&amp;gt;           hc |   0.05 |   1.01\nligandHybridTop__log_&amp;gt; Atom....:   26            hc |   0.05 |   1.01 -&amp;gt;           hc |   0.05 |   1.01\nligandHybridTop__log_&amp;gt; Atom....:    3            os |  -0.44 |  16.00 -&amp;gt;           os |  -0.44 |  16.00\nligandHybridTop__log_&amp;gt; Atom....:    4            ca |   0.74 |  12.01 -&amp;gt;           ca |   0.74 |  12.01\nligandHybridTop__log_&amp;gt; Atom....:    5            nb |  -0.83 |  14.01 -&amp;gt;           nb |  -0.83 |  14.01\nligandHybridTop__log_&amp;gt; Atom....:    6            ca |   0.63 |  12.01 -&amp;gt;           ca |   0.62 |  12.01\nligandHybridTop__log_&amp;gt; Atom....:    7            ca |  -0.39 |  12.01 -&amp;gt;           ca |  -0.39 |  12.01\nligandHybridTop__log_&amp;gt; Atom....:   29            ha |   0.18 |   1.01 -&amp;gt;           ha |   0.18 |   1.01\nligandHybridTop__log_&amp;gt; Atom....:    8            ca |   0.31 |  12.01 -&amp;gt;           ca |   0.31 |  12.01\nligandHybridTop__log_&amp;gt; Atom....:   10            ca |  -0.28 |  12.01 -&amp;gt;           ca |  -0.28 |  12.01\nligandHybridTop__log_&amp;gt; Atom....:   11            cg |   0.27 |  12.01 -&amp;gt;           cg |   0.27 |  12.01\nligandHybridTop__log_&amp;gt; Atom....:   12            n1 |  -0.39 |  14.01 -&amp;gt;           n1 |  -0.39 |  14.01\nligandHybridTop__log_&amp;gt; Atom....:    9            nv |  -0.86 |  14.01 -&amp;gt;           nv |  -0.86 |  14.01\nligandHybridTop__log_&amp;gt; Atom....:   13            ns |  -0.55 |  14.01 -&amp;gt;           ns |  -0.55 |  14.01\nligandHybridTop__log_&amp;gt; Atom....:   14             c |   0.68 |  12.01 -&amp;gt;            c |   0.67 |  12.01\nligandHybridTop__log_&amp;gt; Atom....:   15             o |  -0.58 |  16.00 -&amp;gt;            o |  -0.58 |  16.00\nligandHybridTop__log_&amp;gt; Atom....:   16            c3 |  -0.11 |  12.01 -&amp;gt;           c3 |  -0.11 |  12.01\nligandHybridTop__log_&amp;gt; Atom....:   33            hc |   0.09 |   1.01 -&amp;gt;           hc |   0.09 |   1.01\nligandHybridTop__log_&amp;gt; Atom....:   34            hc |   0.09 |   1.01 -&amp;gt;           hc |   0.09 |   1.01\nligandHybridTop__log_&amp;gt; Atom....:   17            ca |  -0.10 |  12.01 -&amp;gt;           ca |  -0.09 |  12.01\nligandHybridTop__log_&amp;gt; Atom....:   18            ca |   0.03 |  12.01 -&amp;gt;           ca |  -0.11 |  12.01\nligandHybridTop__log_&amp;gt; Atom....:   20            ca |  -0.12 |  12.01 -&amp;gt;           ca |   0.02 |  12.01\nligandHybridTop__log_&amp;gt; Atom....:   21            ca |  -0.11 |  12.01 -&amp;gt;           ca |  -0.12 |  12.01\nligandHybridTop__log_&amp;gt; Atom....:   36            ha |   0.14 |   1.01 -&amp;gt;           ha |   0.15 |   1.01\nligandHybridTop__log_&amp;gt; Atom....:   22            ca |  -0.12 |  12.01 -&amp;gt;           ca |  -0.12 |  12.01\nligandHybridTop__log_&amp;gt; Atom....:   37            ha |   0.14 |   1.01 -&amp;gt;           ha |   0.14 |   1.01\nligandHybridTop__log_&amp;gt; Atom....:   23            ca |  -0.12 |  12.01 -&amp;gt;           ca |  -0.13 |  12.01\nligandHybridTop__log_&amp;gt; Atom....:   38            ha |   0.14 |   1.01 -&amp;gt;           ha |   0.14 |   1.01\nligandHybridTop__log_&amp;gt; Constructing dummies....\nligandHybridTop__log_&amp;gt; Dummies in stateA: \nligandHybridTop__log_&amp;gt; Dummy...:   40        DUM_cl |   0.00 |  35.45 -&amp;gt;           cl |  -0.12 |  35.45\nligandHybridTop__log_&amp;gt; Dummy...:   41        DUM_hn |   0.00 |   1.01 -&amp;gt;           hn |   0.44 |   1.01\nligandHybridTop__log_&amp;gt; Dummy...:   42        DUM_hn |   0.00 |   1.01 -&amp;gt;           hn |   0.44 |   1.01\nligandHybridTop__log_&amp;gt; Dummy...:   43        DUM_hn |   0.00 |   1.01 -&amp;gt;           hn |   0.34 |   1.01\nligandHybridTop__log_&amp;gt; Dummy...:   44        DUM_ha |   0.00 |   1.01 -&amp;gt;           ha |   0.16 |   1.01\nligandHybridTop__log_&amp;gt; Dummy...:   45        DUM_DU |   0.00 |   0.00 -&amp;gt;           DU |   0.04 |   0.00\nligandHybridTop__log_&amp;gt; Dummies in stateB: \nligandHybridTop__log_&amp;gt; Dummy...:   19            cl |  -0.11 |  35.45 -&amp;gt;       DUM_cl |   0.00 |  35.45\nligandHybridTop__log_&amp;gt; Dummy...:   30            hn |   0.44 |   1.01 -&amp;gt;       DUM_hn |   0.00 |   1.01\nligandHybridTop__log_&amp;gt; Dummy...:   31            hn |   0.44 |   1.01 -&amp;gt;       DUM_hn |   0.00 |   1.01\nligandHybridTop__log_&amp;gt; Dummy...:   32            hn |   0.34 |   1.01 -&amp;gt;       DUM_hn |   0.00 |   1.01\nligandHybridTop__log_&amp;gt; Dummy...:   35            ha |   0.15 |   1.01 -&amp;gt;       DUM_ha |   0.00 |   1.01\nligandHybridTop__log_&amp;gt; Dummy...:   39            DU |   0.04 |   0.00 -&amp;gt;       DUM_DU |   0.00 |   0.00\nligandHybridTop__log_&amp;gt; Construct bonds....\nligandHybridTop__log_&amp;gt; Construct angles....\nligandHybridTop__log_&amp;gt; Construct dihedrals....\nligandHybridTop__log_&amp;gt; Construct vsites2....\nligandHybridTop__log_&amp;gt; Construct vsites3....\nligandHybridTop__log_&amp;gt; Construct exclusions....\nligandHybridTop__log_&amp;gt; Construct pairs (1-4 interactions)....\nligandHybridTop__log_&amp;gt; Assembling new itp....\nligandHybridTop__log_&amp;gt; Writing new itp file: &amp;quot;/tmp/biobb/unitests_29/pmxligand_hybrid/sandbox_e8f90aaa-e96b-4458-9806-251ef62c4e19/hybridTopo.itp&amp;quot;\nligandHybridTop__log_&amp;gt; Writing dummy forcefield file: &amp;quot;/tmp/biobb/unitests_29/pmxligand_hybrid/sandbox_e8f90aaa-e96b-4458-9806-251ef62c4e19/hybridAtomTypes.itp&amp;quot;\n\nINFO     /tmp/biobb/unitests_29/pmxligand_hybrid/pmxligand_hybrid_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_29/pmxligand_hybrid/sandbox_e8f90aaa-e96b-4458-9806-251ef62c4e19&amp;#x27;]\nINFO     /tmp/biobb/unitests_29/pmxligand_hybrid/pmxligand_hybrid_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_29\n&#34;}], &#34;biobb_pmx/test/unitests/test_pmx/test_pmxmerge_ff.py::TestPmxmerge_ff::test_pmxmerge_ff&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_pmx/test/unitests/test_pmx/test_pmxmerge_ff.py::TestPmxmerge_ff::test_pmxmerge_ff&#34;, &#34;duration&#34;: &#34;32 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_pmx/test/unitests/test_pmx/test_pmxmerge_ff.py::TestPmxmerge_ff::test_pmxmerge_ff&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;32 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-11-04 14:30:21,911 [MainThread  ] [INFO ]  Module: biobb_pmx.pmxbiobb.pmxmerge_ff Version: 4.2.1\n2024-11-04 14:30:21,911 [MainThread  ] [INFO ]  /tmp/biobb/unitests_29/pmxmerge_ff/sandbox_ccb2f8da-6dc2-4f6a-992b-43125d0cfa86 directory successfully created\n2024-11-04 14:30:21,912 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/itps_to_merge.zip to /tmp/biobb/unitests_29/pmxmerge_ff/sandbox_ccb2f8da-6dc2-4f6a-992b-43125d0cfa86\n2024-11-04 14:30:21,912 [MainThread  ] [INFO ]  Creating 670e809f-9640-4fcc-98a7-b7b92ea9e448 temporary folder\n2024-11-04 14:30:21,912 [MainThread  ] [INFO ]  Extracting: /tmp/biobb/unitests_29/pmxmerge_ff/sandbox_ccb2f8da-6dc2-4f6a-992b-43125d0cfa86/itps_to_merge.zip\n2024-11-04 14:30:21,912 [MainThread  ] [INFO ]  to:\n2024-11-04 14:30:21,913 [MainThread  ] [INFO ]  [&amp;#x27;670e809f-9640-4fcc-98a7-b7b92ea9e448/myHybridAtomTypes.itp&amp;#x27;, &amp;#x27;670e809f-9640-4fcc-98a7-b7b92ea9e448/lig1ffMOL.itp&amp;#x27;, &amp;#x27;670e809f-9640-4fcc-98a7-b7b92ea9e448/lig2ffMOL.itp&amp;#x27;]\n2024-11-04 14:30:21,913 [MainThread  ] [INFO ]  Running merge_FF_files from pmx package...\n\n2024-11-04 14:30:21,913 [MainThread  ] [INFO ]  Exit code 0\n\n2024-11-04 14:30:21,914 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_29/pmxmerge_ff/sandbox_ccb2f8da-6dc2-4f6a-992b-43125d0cfa86&amp;#x27;]\n2024-11-04 14:30:21,914 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_29/pmxmerge_ff/hybridTopo.itp\nComparing size of both files:\n     FILE_A: /tmp/biobb/unitests_29/pmxmerge_ff/hybridTopo.itp\n     FILE_B: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/reference/pmx/ref_mergedTopology.itp\n     SIZE_A: 1468 bytes\n     SIZE_B: 1468 bytes\n     TOLERANCE: 1.0%, Low: 1453.32 bytes, High: 1482.68 bytes\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_29/pmxmerge_ff/pmxmerge_ff_log.out:file_utils.py:409 Module: biobb_pmx.pmxbiobb.pmxmerge_ff Version: 4.2.1\nINFO     /tmp/biobb/unitests_29/pmxmerge_ff/pmxmerge_ff_log.out:file_utils.py:82 /tmp/biobb/unitests_29/pmxmerge_ff/sandbox_ccb2f8da-6dc2-4f6a-992b-43125d0cfa86 directory successfully created\nINFO     /tmp/biobb/unitests_29/pmxmerge_ff/pmxmerge_ff_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/itps_to_merge.zip to /tmp/biobb/unitests_29/pmxmerge_ff/sandbox_ccb2f8da-6dc2-4f6a-992b-43125d0cfa86\nINFO     /tmp/biobb/unitests_29/pmxmerge_ff/pmxmerge_ff_log.out:file_utils.py:409 Creating 670e809f-9640-4fcc-98a7-b7b92ea9e448 temporary folder\nINFO     /tmp/biobb/unitests_29/pmxmerge_ff/pmxmerge_ff_log.out:file_utils.py:172 Extracting: /tmp/biobb/unitests_29/pmxmerge_ff/sandbox_ccb2f8da-6dc2-4f6a-992b-43125d0cfa86/itps_to_merge.zip\nINFO     /tmp/biobb/unitests_29/pmxmerge_ff/pmxmerge_ff_log.out:file_utils.py:173 to:\nINFO     /tmp/biobb/unitests_29/pmxmerge_ff/pmxmerge_ff_log.out:file_utils.py:174 [&amp;#x27;670e809f-9640-4fcc-98a7-b7b92ea9e448/myHybridAtomTypes.itp&amp;#x27;, &amp;#x27;670e809f-9640-4fcc-98a7-b7b92ea9e448/lig1ffMOL.itp&amp;#x27;, &amp;#x27;670e809f-9640-4fcc-98a7-b7b92ea9e448/lig2ffMOL.itp&amp;#x27;]\nINFO     /tmp/biobb/unitests_29/pmxmerge_ff/pmxmerge_ff_log.out:file_utils.py:409 Running merge_FF_files from pmx package...\n\nINFO     /tmp/biobb/unitests_29/pmxmerge_ff/pmxmerge_ff_log.out:file_utils.py:409 Exit code 0\n\nINFO     /tmp/biobb/unitests_29/pmxmerge_ff/pmxmerge_ff_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_29/pmxmerge_ff/sandbox_ccb2f8da-6dc2-4f6a-992b-43125d0cfa86&amp;#x27;]\nINFO     /tmp/biobb/unitests_29/pmxmerge_ff/pmxmerge_ff_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_29\n&#34;}], &#34;biobb_pmx/test/unitests/test_pmx/test_pmxmutate.py::TestPmxmutate::test_pmxmutate&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_pmx/test/unitests/test_pmx/test_pmxmutate.py::TestPmxmutate::test_pmxmutate&#34;, &#34;duration&#34;: &#34;00:00:05&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_pmx/test/unitests/test_pmx/test_pmxmutate.py::TestPmxmutate::test_pmxmutate&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:00:05&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-11-04 14:30:21,944 [MainThread  ] [INFO ]  Module: biobb_pmx.pmxbiobb.pmxmutate Version: 4.2.1\n2024-11-04 14:30:21,944 [MainThread  ] [INFO ]  /tmp/biobb/unitests_29/pmxmutate/sandbox_f7f84cf0-c1d9-4886-9af6-64b1bd7eab1a directory successfully created\n2024-11-04 14:30:21,946 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/frameA0.pdb to /tmp/biobb/unitests_29/pmxmutate/sandbox_f7f84cf0-c1d9-4886-9af6-64b1bd7eab1a\n2024-11-04 14:30:21,947 [MainThread  ] [INFO ]  pmx mutate -f /tmp/biobb/unitests_29/pmxmutate/sandbox_f7f84cf0-c1d9-4886-9af6-64b1bd7eab1a/frameA0.pdb -o /tmp/biobb/unitests_29/pmxmutate/sandbox_f7f84cf0-c1d9-4886-9af6-64b1bd7eab1a/output_structure.pdb -ff amber99sb-star-ildn-mut --script 1ee797e5-b871-40e2-9cde-705af5e41e20/mutations.txt\n\n2024-11-04 14:30:24,922 [MainThread  ] [INFO ]  Executing: pmx mutate -f /tmp/biobb/unitests_29/pmxmutate/sandbox_f7f84cf0-c1d9-4886-9af6-6...\n2024-11-04 14:30:24,922 [MainThread  ] [INFO ]  Exit code: 0\n2024-11-04 14:30:24,922 [MainThread  ] [INFO ]  log_&amp;gt; Residue to mutate: 10 | ILE | A \nlog_&amp;gt; Mutation to apply: I-&amp;gt;A\nlog_&amp;gt; Hybrid residue name: I2A\nlog_&amp;gt; Inserted hybrid residue I2A at position 10 (chain A)\n\nmutations done...........\n\n\n2024-11-04 14:30:24,925 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_29/pmxmutate/sandbox_f7f84cf0-c1d9-4886-9af6-64b1bd7eab1a&amp;#x27;]\n2024-11-04 14:30:24,926 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_29/pmxmutate/output_structure.pdb\nChecking RMSD between:\n     PDB_A: /tmp/biobb/unitests_29/pmxmutate/output_structure.pdb\n     PDB_B: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/reference/pmx/ref_output_structure.pdb\n     Ignoring HETAMT in RMSD\n     Ignoring Hydrogen atoms in RMSD\n     Atoms ALIGNED in PDB_A: 11092\n     Atoms ALIGNED in PDB_B: 11092\n     RMS: 2.2084949513674e-14\n     RMS_CUTOFF: 1\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_29/pmxmutate/pmxmutate_log.out:file_utils.py:409 Module: biobb_pmx.pmxbiobb.pmxmutate Version: 4.2.1\nINFO     /tmp/biobb/unitests_29/pmxmutate/pmxmutate_log.out:file_utils.py:82 /tmp/biobb/unitests_29/pmxmutate/sandbox_f7f84cf0-c1d9-4886-9af6-64b1bd7eab1a directory successfully created\nINFO     /tmp/biobb/unitests_29/pmxmutate/pmxmutate_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/frameA0.pdb to /tmp/biobb/unitests_29/pmxmutate/sandbox_f7f84cf0-c1d9-4886-9af6-64b1bd7eab1a\nINFO     /tmp/biobb/unitests_29/pmxmutate/pmxmutate_log.out:cmd_wrapper.py:63 pmx mutate -f /tmp/biobb/unitests_29/pmxmutate/sandbox_f7f84cf0-c1d9-4886-9af6-64b1bd7eab1a/frameA0.pdb -o /tmp/biobb/unitests_29/pmxmutate/sandbox_f7f84cf0-c1d9-4886-9af6-64b1bd7eab1a/output_structure.pdb -ff amber99sb-star-ildn-mut --script 1ee797e5-b871-40e2-9cde-705af5e41e20/mutations.txt\n\nINFO     /tmp/biobb/unitests_29/pmxmutate/pmxmutate_log.out:cmd_wrapper.py:36 Executing: pmx mutate -f /tmp/biobb/unitests_29/pmxmutate/sandbox_f7f84cf0-c1d9-4886-9af6-6...\nINFO     /tmp/biobb/unitests_29/pmxmutate/pmxmutate_log.out:cmd_wrapper.py:37 Exit code: 0\nINFO     /tmp/biobb/unitests_29/pmxmutate/pmxmutate_log.out:cmd_wrapper.py:41 log_&amp;gt; Residue to mutate: 10 | ILE | A \nlog_&amp;gt; Mutation to apply: I-&amp;gt;A\nlog_&amp;gt; Hybrid residue name: I2A\nlog_&amp;gt; Inserted hybrid residue I2A at position 10 (chain A)\n\nmutations done...........\n\n\nINFO     /tmp/biobb/unitests_29/pmxmutate/pmxmutate_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_29/pmxmutate/sandbox_f7f84cf0-c1d9-4886-9af6-64b1bd7eab1a&amp;#x27;]\nINFO     /tmp/biobb/unitests_29/pmxmutate/pmxmutate_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_29\n&#34;}]}, &#34;renderCollapsed&#34;: [&#34;passed&#34;], &#34;initialSort&#34;: &#34;result&#34;, &#34;title&#34;: &#34;report.html&#34;}"></div>
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&#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:00:13&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-11-04 15:32:57,449 [MainThread  ] [INFO ]  Module: biobb_pmx.pmxbiobb.pmxanalyse Version: 4.2.1\n2024-11-04 15:32:57,449 [MainThread  ] [INFO ]  /tmp/biobb/unitests_35/pmxanalyse/sandbox_caa2a2bb-d1c7-4712-91de-2bfa47012916 directory successfully created\n2024-11-04 15:32:57,714 [MainThread  ] [INFO ]  Extracting: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/xvg_A.zip\n2024-11-04 15:32:57,714 [MainThread  ] [INFO ]  to:\n2024-11-04 15:32:57,715 [MainThread  ] [INFO ]  [&amp;#x27;fa78b971-e0cd-4f42-99d6-53c37047af6d/frame0/dhdl0.xvg&amp;#x27;, &amp;#x27;fa78b971-e0cd-4f42-99d6-53c37047af6d/frame1/dhdl1.xvg&amp;#x27;, &amp;#x27;fa78b971-e0cd-4f42-99d6-53c37047af6d/frame10/dhdl10.xvg&amp;#x27;, 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&amp;#x27;fa78b971-e0cd-4f42-99d6-53c37047af6d/frame82/dhdl82.xvg&amp;#x27;, &amp;#x27;fa78b971-e0cd-4f42-99d6-53c37047af6d/frame83/dhdl83.xvg&amp;#x27;, &amp;#x27;fa78b971-e0cd-4f42-99d6-53c37047af6d/frame84/dhdl84.xvg&amp;#x27;, &amp;#x27;fa78b971-e0cd-4f42-99d6-53c37047af6d/frame85/dhdl85.xvg&amp;#x27;, &amp;#x27;fa78b971-e0cd-4f42-99d6-53c37047af6d/frame86/dhdl86.xvg&amp;#x27;, &amp;#x27;fa78b971-e0cd-4f42-99d6-53c37047af6d/frame87/dhdl87.xvg&amp;#x27;, &amp;#x27;fa78b971-e0cd-4f42-99d6-53c37047af6d/frame88/dhdl88.xvg&amp;#x27;, &amp;#x27;fa78b971-e0cd-4f42-99d6-53c37047af6d/frame89/dhdl89.xvg&amp;#x27;, &amp;#x27;fa78b971-e0cd-4f42-99d6-53c37047af6d/frame9/dhdl9.xvg&amp;#x27;, &amp;#x27;fa78b971-e0cd-4f42-99d6-53c37047af6d/frame90/dhdl90.xvg&amp;#x27;, &amp;#x27;fa78b971-e0cd-4f42-99d6-53c37047af6d/frame91/dhdl91.xvg&amp;#x27;, &amp;#x27;fa78b971-e0cd-4f42-99d6-53c37047af6d/frame92/dhdl92.xvg&amp;#x27;, &amp;#x27;fa78b971-e0cd-4f42-99d6-53c37047af6d/frame93/dhdl93.xvg&amp;#x27;, &amp;#x27;fa78b971-e0cd-4f42-99d6-53c37047af6d/frame94/dhdl94.xvg&amp;#x27;, &amp;#x27;fa78b971-e0cd-4f42-99d6-53c37047af6d/frame95/dhdl95.xvg&amp;#x27;, &amp;#x27;fa78b971-e0cd-4f42-99d6-53c37047af6d/frame96/dhdl96.xvg&amp;#x27;, &amp;#x27;fa78b971-e0cd-4f42-99d6-53c37047af6d/frame97/dhdl97.xvg&amp;#x27;, &amp;#x27;fa78b971-e0cd-4f42-99d6-53c37047af6d/frame98/dhdl98.xvg&amp;#x27;, &amp;#x27;fa78b971-e0cd-4f42-99d6-53c37047af6d/frame99/dhdl99.xvg&amp;#x27;]\n2024-11-04 15:32:58,009 [MainThread  ] [INFO ]  Extracting: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/xvg_B.zip\n2024-11-04 15:32:58,009 [MainThread  ] [INFO ]  to:\n2024-11-04 15:32:58,009 [MainThread  ] [INFO ]  [&amp;#x27;7f115544-785b-40d7-ad77-b07c2aa09840/frame0/dhdl0.xvg&amp;#x27;, &amp;#x27;7f115544-785b-40d7-ad77-b07c2aa09840/frame1/dhdl1.xvg&amp;#x27;, &amp;#x27;7f115544-785b-40d7-ad77-b07c2aa09840/frame10/dhdl10.xvg&amp;#x27;, &amp;#x27;7f115544-785b-40d7-ad77-b07c2aa09840/frame11/dhdl11.xvg&amp;#x27;, &amp;#x27;7f115544-785b-40d7-ad77-b07c2aa09840/frame12/dhdl12.xvg&amp;#x27;, &amp;#x27;7f115544-785b-40d7-ad77-b07c2aa09840/frame13/dhdl13.xvg&amp;#x27;, &amp;#x27;7f115544-785b-40d7-ad77-b07c2aa09840/frame14/dhdl14.xvg&amp;#x27;, &amp;#x27;7f115544-785b-40d7-ad77-b07c2aa09840/frame15/dhdl15.xvg&amp;#x27;, &amp;#x27;7f115544-785b-40d7-ad77-b07c2aa09840/frame16/dhdl16.xvg&amp;#x27;, &amp;#x27;7f115544-785b-40d7-ad77-b07c2aa09840/frame17/dhdl17.xvg&amp;#x27;, &amp;#x27;7f115544-785b-40d7-ad77-b07c2aa09840/frame18/dhdl18.xvg&amp;#x27;, &amp;#x27;7f115544-785b-40d7-ad77-b07c2aa09840/frame19/dhdl19.xvg&amp;#x27;, &amp;#x27;7f115544-785b-40d7-ad77-b07c2aa09840/frame2/dhdl2.xvg&amp;#x27;, &amp;#x27;7f115544-785b-40d7-ad77-b07c2aa09840/frame20/dhdl20.xvg&amp;#x27;, &amp;#x27;7f115544-785b-40d7-ad77-b07c2aa09840/frame21/dhdl21.xvg&amp;#x27;, &amp;#x27;7f115544-785b-40d7-ad77-b07c2aa09840/frame22/dhdl22.xvg&amp;#x27;, &amp;#x27;7f115544-785b-40d7-ad77-b07c2aa09840/frame23/dhdl23.xvg&amp;#x27;, &amp;#x27;7f115544-785b-40d7-ad77-b07c2aa09840/frame24/dhdl24.xvg&amp;#x27;, &amp;#x27;7f115544-785b-40d7-ad77-b07c2aa09840/frame25/dhdl25.xvg&amp;#x27;, &amp;#x27;7f115544-785b-40d7-ad77-b07c2aa09840/frame26/dhdl26.xvg&amp;#x27;, &amp;#x27;7f115544-785b-40d7-ad77-b07c2aa09840/frame27/dhdl27.xvg&amp;#x27;, &amp;#x27;7f115544-785b-40d7-ad77-b07c2aa09840/frame28/dhdl28.xvg&amp;#x27;, &amp;#x27;7f115544-785b-40d7-ad77-b07c2aa09840/frame29/dhdl29.xvg&amp;#x27;, &amp;#x27;7f115544-785b-40d7-ad77-b07c2aa09840/frame3/dhdl3.xvg&amp;#x27;, &amp;#x27;7f115544-785b-40d7-ad77-b07c2aa09840/frame30/dhdl30.xvg&amp;#x27;, &amp;#x27;7f115544-785b-40d7-ad77-b07c2aa09840/frame31/dhdl31.xvg&amp;#x27;, &amp;#x27;7f115544-785b-40d7-ad77-b07c2aa09840/frame32/dhdl32.xvg&amp;#x27;, &amp;#x27;7f115544-785b-40d7-ad77-b07c2aa09840/frame33/dhdl33.xvg&amp;#x27;, &amp;#x27;7f115544-785b-40d7-ad77-b07c2aa09840/frame34/dhdl34.xvg&amp;#x27;, &amp;#x27;7f115544-785b-40d7-ad77-b07c2aa09840/frame35/dhdl35.xvg&amp;#x27;, &amp;#x27;7f115544-785b-40d7-ad77-b07c2aa09840/frame36/dhdl36.xvg&amp;#x27;, &amp;#x27;7f115544-785b-40d7-ad77-b07c2aa09840/frame37/dhdl37.xvg&amp;#x27;, &amp;#x27;7f115544-785b-40d7-ad77-b07c2aa09840/frame38/dhdl38.xvg&amp;#x27;, &amp;#x27;7f115544-785b-40d7-ad77-b07c2aa09840/frame39/dhdl39.xvg&amp;#x27;, &amp;#x27;7f115544-785b-40d7-ad77-b07c2aa09840/frame4/dhdl4.xvg&amp;#x27;, &amp;#x27;7f115544-785b-40d7-ad77-b07c2aa09840/frame40/dhdl40.xvg&amp;#x27;, &amp;#x27;7f115544-785b-40d7-ad77-b07c2aa09840/frame41/dhdl41.xvg&amp;#x27;, &amp;#x27;7f115544-785b-40d7-ad77-b07c2aa09840/frame42/dhdl42.xvg&amp;#x27;, &amp;#x27;7f115544-785b-40d7-ad77-b07c2aa09840/frame43/dhdl43.xvg&amp;#x27;, &amp;#x27;7f115544-785b-40d7-ad77-b07c2aa09840/frame44/dhdl44.xvg&amp;#x27;, &amp;#x27;7f115544-785b-40d7-ad77-b07c2aa09840/frame45/dhdl45.xvg&amp;#x27;, &amp;#x27;7f115544-785b-40d7-ad77-b07c2aa09840/frame46/dhdl46.xvg&amp;#x27;, &amp;#x27;7f115544-785b-40d7-ad77-b07c2aa09840/frame47/dhdl47.xvg&amp;#x27;, &amp;#x27;7f115544-785b-40d7-ad77-b07c2aa09840/frame48/dhdl48.xvg&amp;#x27;, &amp;#x27;7f115544-785b-40d7-ad77-b07c2aa09840/frame49/dhdl49.xvg&amp;#x27;, &amp;#x27;7f115544-785b-40d7-ad77-b07c2aa09840/frame5/dhdl5.xvg&amp;#x27;, &amp;#x27;7f115544-785b-40d7-ad77-b07c2aa09840/frame50/dhdl50.xvg&amp;#x27;, &amp;#x27;7f115544-785b-40d7-ad77-b07c2aa09840/frame51/dhdl51.xvg&amp;#x27;, &amp;#x27;7f115544-785b-40d7-ad77-b07c2aa09840/frame52/dhdl52.xvg&amp;#x27;, &amp;#x27;7f115544-785b-40d7-ad77-b07c2aa09840/frame53/dhdl53.xvg&amp;#x27;, &amp;#x27;7f115544-785b-40d7-ad77-b07c2aa09840/frame54/dhdl54.xvg&amp;#x27;, &amp;#x27;7f115544-785b-40d7-ad77-b07c2aa09840/frame55/dhdl55.xvg&amp;#x27;, &amp;#x27;7f115544-785b-40d7-ad77-b07c2aa09840/frame56/dhdl56.xvg&amp;#x27;, &amp;#x27;7f115544-785b-40d7-ad77-b07c2aa09840/frame57/dhdl57.xvg&amp;#x27;, &amp;#x27;7f115544-785b-40d7-ad77-b07c2aa09840/frame58/dhdl58.xvg&amp;#x27;, &amp;#x27;7f115544-785b-40d7-ad77-b07c2aa09840/frame59/dhdl59.xvg&amp;#x27;, &amp;#x27;7f115544-785b-40d7-ad77-b07c2aa09840/frame6/dhdl6.xvg&amp;#x27;, &amp;#x27;7f115544-785b-40d7-ad77-b07c2aa09840/frame60/dhdl60.xvg&amp;#x27;, &amp;#x27;7f115544-785b-40d7-ad77-b07c2aa09840/frame61/dhdl61.xvg&amp;#x27;, &amp;#x27;7f115544-785b-40d7-ad77-b07c2aa09840/frame62/dhdl62.xvg&amp;#x27;, &amp;#x27;7f115544-785b-40d7-ad77-b07c2aa09840/frame63/dhdl63.xvg&amp;#x27;, &amp;#x27;7f115544-785b-40d7-ad77-b07c2aa09840/frame64/dhdl64.xvg&amp;#x27;, &amp;#x27;7f115544-785b-40d7-ad77-b07c2aa09840/frame65/dhdl65.xvg&amp;#x27;, &amp;#x27;7f115544-785b-40d7-ad77-b07c2aa09840/frame66/dhdl66.xvg&amp;#x27;, &amp;#x27;7f115544-785b-40d7-ad77-b07c2aa09840/frame67/dhdl67.xvg&amp;#x27;, &amp;#x27;7f115544-785b-40d7-ad77-b07c2aa09840/frame68/dhdl68.xvg&amp;#x27;, &amp;#x27;7f115544-785b-40d7-ad77-b07c2aa09840/frame69/dhdl69.xvg&amp;#x27;, &amp;#x27;7f115544-785b-40d7-ad77-b07c2aa09840/frame7/dhdl7.xvg&amp;#x27;, &amp;#x27;7f115544-785b-40d7-ad77-b07c2aa09840/frame70/dhdl70.xvg&amp;#x27;, &amp;#x27;7f115544-785b-40d7-ad77-b07c2aa09840/frame71/dhdl71.xvg&amp;#x27;, &amp;#x27;7f115544-785b-40d7-ad77-b07c2aa09840/frame72/dhdl72.xvg&amp;#x27;, &amp;#x27;7f115544-785b-40d7-ad77-b07c2aa09840/frame73/dhdl73.xvg&amp;#x27;, &amp;#x27;7f115544-785b-40d7-ad77-b07c2aa09840/frame74/dhdl74.xvg&amp;#x27;, &amp;#x27;7f115544-785b-40d7-ad77-b07c2aa09840/frame75/dhdl75.xvg&amp;#x27;, &amp;#x27;7f115544-785b-40d7-ad77-b07c2aa09840/frame76/dhdl76.xvg&amp;#x27;, &amp;#x27;7f115544-785b-40d7-ad77-b07c2aa09840/frame77/dhdl77.xvg&amp;#x27;, &amp;#x27;7f115544-785b-40d7-ad77-b07c2aa09840/frame78/dhdl78.xvg&amp;#x27;, &amp;#x27;7f115544-785b-40d7-ad77-b07c2aa09840/frame79/dhdl79.xvg&amp;#x27;, &amp;#x27;7f115544-785b-40d7-ad77-b07c2aa09840/frame8/dhdl8.xvg&amp;#x27;, &amp;#x27;7f115544-785b-40d7-ad77-b07c2aa09840/frame80/dhdl80.xvg&amp;#x27;, &amp;#x27;7f115544-785b-40d7-ad77-b07c2aa09840/frame81/dhdl81.xvg&amp;#x27;, &amp;#x27;7f115544-785b-40d7-ad77-b07c2aa09840/frame82/dhdl82.xvg&amp;#x27;, &amp;#x27;7f115544-785b-40d7-ad77-b07c2aa09840/frame83/dhdl83.xvg&amp;#x27;, &amp;#x27;7f115544-785b-40d7-ad77-b07c2aa09840/frame84/dhdl84.xvg&amp;#x27;, &amp;#x27;7f115544-785b-40d7-ad77-b07c2aa09840/frame85/dhdl85.xvg&amp;#x27;, &amp;#x27;7f115544-785b-40d7-ad77-b07c2aa09840/frame86/dhdl86.xvg&amp;#x27;, &amp;#x27;7f115544-785b-40d7-ad77-b07c2aa09840/frame87/dhdl87.xvg&amp;#x27;, &amp;#x27;7f115544-785b-40d7-ad77-b07c2aa09840/frame88/dhdl88.xvg&amp;#x27;, &amp;#x27;7f115544-785b-40d7-ad77-b07c2aa09840/frame89/dhdl89.xvg&amp;#x27;, &amp;#x27;7f115544-785b-40d7-ad77-b07c2aa09840/frame9/dhdl9.xvg&amp;#x27;, &amp;#x27;7f115544-785b-40d7-ad77-b07c2aa09840/frame90/dhdl90.xvg&amp;#x27;, &amp;#x27;7f115544-785b-40d7-ad77-b07c2aa09840/frame91/dhdl91.xvg&amp;#x27;, &amp;#x27;7f115544-785b-40d7-ad77-b07c2aa09840/frame92/dhdl92.xvg&amp;#x27;, &amp;#x27;7f115544-785b-40d7-ad77-b07c2aa09840/frame93/dhdl93.xvg&amp;#x27;, &amp;#x27;7f115544-785b-40d7-ad77-b07c2aa09840/frame94/dhdl94.xvg&amp;#x27;, &amp;#x27;7f115544-785b-40d7-ad77-b07c2aa09840/frame95/dhdl95.xvg&amp;#x27;, &amp;#x27;7f115544-785b-40d7-ad77-b07c2aa09840/frame96/dhdl96.xvg&amp;#x27;, &amp;#x27;7f115544-785b-40d7-ad77-b07c2aa09840/frame97/dhdl97.xvg&amp;#x27;, &amp;#x27;7f115544-785b-40d7-ad77-b07c2aa09840/frame98/dhdl98.xvg&amp;#x27;, &amp;#x27;7f115544-785b-40d7-ad77-b07c2aa09840/frame99/dhdl99.xvg&amp;#x27;]\n2024-11-04 15:32:58,011 [MainThread  ] [INFO ]  pmx analyse -fA fa78b971-e0cd-4f42-99d6-53c37047af6d/frame0/dhdl0.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame1/dhdl1.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame10/dhdl10.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame11/dhdl11.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame12/dhdl12.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame13/dhdl13.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame14/dhdl14.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame15/dhdl15.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame16/dhdl16.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame17/dhdl17.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame18/dhdl18.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame19/dhdl19.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame2/dhdl2.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame20/dhdl20.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame21/dhdl21.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame22/dhdl22.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame23/dhdl23.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame24/dhdl24.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame25/dhdl25.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame26/dhdl26.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame27/dhdl27.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame28/dhdl28.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame29/dhdl29.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame3/dhdl3.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame30/dhdl30.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame31/dhdl31.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame32/dhdl32.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame33/dhdl33.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame34/dhdl34.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame35/dhdl35.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame36/dhdl36.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame37/dhdl37.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame38/dhdl38.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame39/dhdl39.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame4/dhdl4.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame40/dhdl40.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame41/dhdl41.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame42/dhdl42.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame43/dhdl43.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame44/dhdl44.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame45/dhdl45.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame46/dhdl46.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame47/dhdl47.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame48/dhdl48.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame49/dhdl49.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame5/dhdl5.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame50/dhdl50.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame51/dhdl51.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame52/dhdl52.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame53/dhdl53.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame54/dhdl54.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame55/dhdl55.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame56/dhdl56.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame57/dhdl57.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame58/dhdl58.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame59/dhdl59.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame6/dhdl6.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame60/dhdl60.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame61/dhdl61.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame62/dhdl62.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame63/dhdl63.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame64/dhdl64.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame65/dhdl65.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame66/dhdl66.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame67/dhdl67.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame68/dhdl68.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame69/dhdl69.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame7/dhdl7.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame70/dhdl70.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame71/dhdl71.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame72/dhdl72.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame73/dhdl73.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame74/dhdl74.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame75/dhdl75.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame76/dhdl76.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame77/dhdl77.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame78/dhdl78.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame79/dhdl79.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame8/dhdl8.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame80/dhdl80.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame81/dhdl81.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame82/dhdl82.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame83/dhdl83.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame84/dhdl84.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame85/dhdl85.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame86/dhdl86.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame87/dhdl87.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame88/dhdl88.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame89/dhdl89.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame9/dhdl9.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame90/dhdl90.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame91/dhdl91.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame92/dhdl92.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame93/dhdl93.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame94/dhdl94.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame95/dhdl95.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame96/dhdl96.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame97/dhdl97.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame98/dhdl98.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame99/dhdl99.xvg -fB 7f115544-785b-40d7-ad77-b07c2aa09840/frame0/dhdl0.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame1/dhdl1.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame10/dhdl10.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame11/dhdl11.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame12/dhdl12.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame13/dhdl13.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame14/dhdl14.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame15/dhdl15.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame16/dhdl16.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame17/dhdl17.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame18/dhdl18.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame19/dhdl19.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame2/dhdl2.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame20/dhdl20.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame21/dhdl21.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame22/dhdl22.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame23/dhdl23.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame24/dhdl24.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame25/dhdl25.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame26/dhdl26.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame27/dhdl27.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame28/dhdl28.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame29/dhdl29.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame3/dhdl3.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame30/dhdl30.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame31/dhdl31.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame32/dhdl32.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame33/dhdl33.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame34/dhdl34.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame35/dhdl35.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame36/dhdl36.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame37/dhdl37.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame38/dhdl38.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame39/dhdl39.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame4/dhdl4.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame40/dhdl40.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame41/dhdl41.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame42/dhdl42.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame43/dhdl43.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame44/dhdl44.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame45/dhdl45.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame46/dhdl46.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame47/dhdl47.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame48/dhdl48.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame49/dhdl49.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame5/dhdl5.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame50/dhdl50.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame51/dhdl51.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame52/dhdl52.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame53/dhdl53.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame54/dhdl54.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame55/dhdl55.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame56/dhdl56.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame57/dhdl57.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame58/dhdl58.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame59/dhdl59.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame6/dhdl6.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame60/dhdl60.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame61/dhdl61.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame62/dhdl62.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame63/dhdl63.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame64/dhdl64.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame65/dhdl65.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame66/dhdl66.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame67/dhdl67.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame68/dhdl68.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame69/dhdl69.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame7/dhdl7.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame70/dhdl70.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame71/dhdl71.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame72/dhdl72.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame73/dhdl73.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame74/dhdl74.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame75/dhdl75.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame76/dhdl76.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame77/dhdl77.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame78/dhdl78.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame79/dhdl79.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame8/dhdl8.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame80/dhdl80.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame81/dhdl81.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame82/dhdl82.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame83/dhdl83.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame84/dhdl84.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame85/dhdl85.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame86/dhdl86.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame87/dhdl87.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame88/dhdl88.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame89/dhdl89.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame9/dhdl9.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame90/dhdl90.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame91/dhdl91.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame92/dhdl92.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame93/dhdl93.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame94/dhdl94.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame95/dhdl95.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame96/dhdl96.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame97/dhdl97.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame98/dhdl98.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame99/dhdl99.xvg -o /tmp/biobb/unitests_35/pmxanalyse/sandbox_caa2a2bb-d1c7-4712-91de-2bfa47012916/result.txt -w /tmp/biobb/unitests_35/pmxanalyse/sandbox_caa2a2bb-d1c7-4712-91de-2bfa47012916/plot.png -m CGI BAR JARZ -t 298.15 -n 1 --skip 1 --prec 2 --units kJ --nbins 20 --dpi 600\n\n2024-11-04 15:33:09,631 [MainThread  ] [INFO ]  Executing: pmx analyse -fA fa78b971-e0cd-4f42-99d6-53c37047af6d/frame0/dhdl0.xvg fa78b971-e...\n2024-11-04 15:33:09,631 [MainThread  ] [INFO ]  Exit code: 0\n2024-11-04 15:33:09,631 [MainThread  ] [INFO ]  \n\n ========================================================\n                   PROCESSING THE DATA\n ========================================================\n  Forward Data\n    First accepted file: fa78b971-e0cd-4f42-99d6-53c37047af6d/frame0/dhdl0.xvg\n    # data points: 25001\n    Length of trajectory:   50.000 ps\n    Delta lambda:  0.00004\n\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame1/dhdl1.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame2/dhdl2.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame3/dhdl3.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame4/dhdl4.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame5/dhdl5.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame6/dhdl6.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame7/dhdl7.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame8/dhdl8.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame9/dhdl9.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame10/dhdl10.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame11/dhdl11.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame12/dhdl12.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame13/dhdl13.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame14/dhdl14.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame15/dhdl15.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame16/dhdl16.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame17/dhdl17.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame18/dhdl18.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame19/dhdl19.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame20/dhdl20.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame21/dhdl21.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame22/dhdl22.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame23/dhdl23.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame24/dhdl24.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame25/dhdl25.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame26/dhdl26.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame27/dhdl27.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame28/dhdl28.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame29/dhdl29.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame30/dhdl30.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame31/dhdl31.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame32/dhdl32.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame33/dhdl33.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame34/dhdl34.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame35/dhdl35.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame36/dhdl36.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame37/dhdl37.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame38/dhdl38.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame39/dhdl39.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame40/dhdl40.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame41/dhdl41.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame42/dhdl42.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame43/dhdl43.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame44/dhdl44.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame45/dhdl45.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame46/dhdl46.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame47/dhdl47.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame48/dhdl48.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame49/dhdl49.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame50/dhdl50.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame51/dhdl51.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame52/dhdl52.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame53/dhdl53.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame54/dhdl54.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame55/dhdl55.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame56/dhdl56.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame57/dhdl57.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame58/dhdl58.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame59/dhdl59.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame60/dhdl60.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame61/dhdl61.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame62/dhdl62.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame63/dhdl63.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame64/dhdl64.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame65/dhdl65.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame66/dhdl66.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame67/dhdl67.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame68/dhdl68.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame69/dhdl69.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame70/dhdl70.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame71/dhdl71.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame72/dhdl72.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame73/dhdl73.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame74/dhdl74.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame75/dhdl75.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame76/dhdl76.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame77/dhdl77.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame78/dhdl78.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame79/dhdl79.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame80/dhdl80.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame81/dhdl81.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame82/dhdl82.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame83/dhdl83.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame84/dhdl84.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame85/dhdl85.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame86/dhdl86.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame87/dhdl87.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame88/dhdl88.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame89/dhdl89.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame90/dhdl90.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame91/dhdl91.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame92/dhdl92.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame93/dhdl93.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame94/dhdl94.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame95/dhdl95.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame96/dhdl96.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame97/dhdl97.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame98/dhdl98.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame99/dhdl99.xvg\n\n  Reverse Data\n    First accepted file: 7f115544-785b-40d7-ad77-b07c2aa09840/frame0/dhdl0.xvg\n    # data points: 25001\n    Length of trajectory:   50.000 ps\n    Delta lambda: -0.00004\n\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame1/dhdl1.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame2/dhdl2.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame3/dhdl3.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame4/dhdl4.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame5/dhdl5.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame6/dhdl6.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame7/dhdl7.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame8/dhdl8.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame9/dhdl9.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame10/dhdl10.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame11/dhdl11.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame12/dhdl12.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame13/dhdl13.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame14/dhdl14.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame15/dhdl15.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame16/dhdl16.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame17/dhdl17.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame18/dhdl18.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame19/dhdl19.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame20/dhdl20.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame21/dhdl21.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame22/dhdl22.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame23/dhdl23.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame24/dhdl24.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame25/dhdl25.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame26/dhdl26.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame27/dhdl27.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame28/dhdl28.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame29/dhdl29.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame30/dhdl30.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame31/dhdl31.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame32/dhdl32.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame33/dhdl33.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame34/dhdl34.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame35/dhdl35.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame36/dhdl36.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame37/dhdl37.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame38/dhdl38.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame39/dhdl39.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame40/dhdl40.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame41/dhdl41.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame42/dhdl42.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame43/dhdl43.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame44/dhdl44.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame45/dhdl45.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame46/dhdl46.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame47/dhdl47.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame48/dhdl48.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame49/dhdl49.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame50/dhdl50.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame51/dhdl51.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame52/dhdl52.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame53/dhdl53.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame54/dhdl54.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame55/dhdl55.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame56/dhdl56.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame57/dhdl57.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame58/dhdl58.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame59/dhdl59.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame60/dhdl60.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame61/dhdl61.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame62/dhdl62.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame63/dhdl63.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame64/dhdl64.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame65/dhdl65.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame66/dhdl66.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame67/dhdl67.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame68/dhdl68.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame69/dhdl69.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame70/dhdl70.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame71/dhdl71.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame72/dhdl72.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame73/dhdl73.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame74/dhdl74.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame75/dhdl75.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame76/dhdl76.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame77/dhdl77.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame78/dhdl78.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame79/dhdl79.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame80/dhdl80.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame81/dhdl81.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame82/dhdl82.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame83/dhdl83.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame84/dhdl84.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame85/dhdl85.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame86/dhdl86.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame87/dhdl87.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame88/dhdl88.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame89/dhdl89.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame90/dhdl90.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame91/dhdl91.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame92/dhdl92.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame93/dhdl93.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame94/dhdl94.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame95/dhdl95.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame96/dhdl96.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame97/dhdl97.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame98/dhdl98.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame99/dhdl99.xvg\n\n ========================================================\n                       ANALYSIS\n ========================================================\n  Number of forward (0-&amp;gt;1) trajectories: 100\n  Number of reverse (1-&amp;gt;0) trajectories: 100\n  Temperature : 298.15 K\n\n --------------------------------------------------------\n             Crooks Gaussian Intersection     \n --------------------------------------------------------\n  Calculating Intersection...\n\r  Bootstrap (Std Err): iteration 1/100\r  Bootstrap (Std Err): iteration 2/100\r  Bootstrap (Std Err): iteration 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Forward Gauss mean =    13.51 kJ/mol std =     4.03 kJ/mol\n  CGI: Reverse Gauss mean =     5.40 kJ/mol std =     8.49 kJ/mol\n  CGI: dG =     8.39 kJ/mol\n  CGI: Std Err (bootstrap:parametric) =     0.42 kJ/mol\n  CGI: Std Err (bootstrap) =     0.43 kJ/mol\n\n  Running KS-test...\n    Forward: gaussian quality = 0.41\n             ---&amp;gt; KS-Test Ok\n    Reverse: gaussian quality = 0.98\n             ---&amp;gt; KS-Test Ok\n\n --------------------------------------------------------\n             Bennett Acceptance Ratio     \n --------------------------------------------------------\n  Running Nelder-Mead Simplex algorithm... \n\r  Bootstrap (Std Err): iteration 1/100\r  Bootstrap (Std Err): iteration 2/100\r  Bootstrap (Std Err): iteration 3/100\r  Bootstrap (Std Err): iteration 4/100\r  Bootstrap (Std Err): iteration 5/100\r  Bootstrap (Std Err): iteration 6/100\r  Bootstrap (Std Err): iteration 7/100\r  Bootstrap (Std Err): iteration 8/100\r  Bootstrap (Std Err): iteration 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Bootstrap (Std Err): iteration 98/100\r  Bootstrap (Std Err): iteration 99/100\r  Bootstrap (Std Err): iteration 100/100\n  JARZ: dG Forward =    10.24 kJ/mol\n  JARZ: dG Reverse =    20.82 kJ/mol\n  JARZ: dG Mean    =    15.53 kJ/mol\n  JARZ: Std Err Forward (bootstrap) =     0.53 kJ/mol\n  JARZ: Std Err Reverse (bootstrap) =     2.69 kJ/mol\n\r  Bootstrap (Std Err): iteration 1/100\r  Bootstrap (Std Err): iteration 2/100\r  Bootstrap (Std Err): iteration 3/100\r  Bootstrap (Std Err): iteration 4/100\r  Bootstrap (Std Err): iteration 5/100\r  Bootstrap (Std Err): iteration 6/100\r  Bootstrap (Std Err): iteration 7/100\r  Bootstrap (Std Err): iteration 8/100\r  Bootstrap (Std Err): iteration 9/100\r  Bootstrap (Std Err): iteration 10/100\r  Bootstrap (Std Err): iteration 11/100\r  Bootstrap (Std Err): iteration 12/100\r  Bootstrap (Std Err): iteration 13/100\r  Bootstrap (Std Err): iteration 14/100\r  Bootstrap (Std Err): iteration 15/100\r  Bootstrap (Std Err): iteration 16/100\r  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Bootstrap (Std Err): iteration 63/100\r  Bootstrap (Std Err): iteration 64/100\r  Bootstrap (Std Err): iteration 65/100\r  Bootstrap (Std Err): iteration 66/100\r  Bootstrap (Std Err): iteration 67/100\r  Bootstrap (Std Err): iteration 68/100\r  Bootstrap (Std Err): iteration 69/100\r  Bootstrap (Std Err): iteration 70/100\r  Bootstrap (Std Err): iteration 71/100\r  Bootstrap (Std Err): iteration 72/100\r  Bootstrap (Std Err): iteration 73/100\r  Bootstrap (Std Err): iteration 74/100\r  Bootstrap (Std Err): iteration 75/100\r  Bootstrap (Std Err): iteration 76/100\r  Bootstrap (Std Err): iteration 77/100\r  Bootstrap (Std Err): iteration 78/100\r  Bootstrap (Std Err): iteration 79/100\r  Bootstrap (Std Err): iteration 80/100\r  Bootstrap (Std Err): iteration 81/100\r  Bootstrap (Std Err): iteration 82/100\r  Bootstrap (Std Err): iteration 83/100\r  Bootstrap (Std Err): iteration 84/100\r  Bootstrap (Std Err): iteration 85/100\r  Bootstrap (Std Err): iteration 86/100\r  Bootstrap (Std Err): iteration 87/100\r  Bootstrap (Std Err): iteration 88/100\r  Bootstrap (Std Err): iteration 89/100\r  Bootstrap (Std Err): iteration 90/100\r  Bootstrap (Std Err): iteration 91/100\r  Bootstrap (Std Err): iteration 92/100\r  Bootstrap (Std Err): iteration 93/100\r  Bootstrap (Std Err): iteration 94/100\r  Bootstrap (Std Err): iteration 95/100\r  Bootstrap (Std Err): iteration 96/100\r  Bootstrap (Std Err): iteration 97/100\r  Bootstrap (Std Err): iteration 98/100\r  Bootstrap (Std Err): iteration 99/100\r  Bootstrap (Std Err): iteration 100/100\n  JARZ_Gauss: dG Forward =    10.19 kJ/mol\n  JARZ_Gauss: dG Reverse =    20.07 kJ/mol\n  JARZ_Gauss: dG Mean    =    15.13 kJ/mol\n  JARZ_Gauss: Std Err (analytical) Forward =     0.62 kJ/mol\n  JARZ_Gauss: Std Err (analytical) Reverse =     2.25 kJ/mol\n  JARZ_Gauss: Std Err Forward (bootstrap) =     0.64 kJ/mol\n  JARZ_Gauss: Std Err Reverse (bootstrap) =     2.45 kJ/mol\n ========================================================\n\n   Plotting histograms......\n\n   ......done...........\n\n   Execution time = 00:00:10\n\n\n2024-11-04 15:33:09,656 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_35/pmxanalyse/sandbox_caa2a2bb-d1c7-4712-91de-2bfa47012916&amp;#x27;, &amp;#x27;fa78b971-e0cd-4f42-99d6-53c37047af6d&amp;#x27;, &amp;#x27;7f115544-785b-40d7-ad77-b07c2aa09840&amp;#x27;]\n2024-11-04 15:33:09,657 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_35/pmxanalyse/result.txt\nChecking if empty file: /tmp/biobb/unitests_35/pmxanalyse/plot.png\nComparing images of both files:\n     IMAGE_A: /tmp/biobb/unitests_35/pmxanalyse/plot.png\n     IMAGE_B: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/reference/pmx/ref_plot.png\n     IMAGE_A HASH: ffdfe78183a7f7df SIZE: 64 bits\n     IMAGE_B HASH: ffdfe78183a7f7df SIZE: 64 bits\n     TOLERANCE: 1.0%, ABS TOLERANCE: 1 bits, DIFFERENCE: 0 bits\n\n------------------------------ Captured log call 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&amp;#x27;fa78b971-e0cd-4f42-99d6-53c37047af6d/frame94/dhdl94.xvg&amp;#x27;, &amp;#x27;fa78b971-e0cd-4f42-99d6-53c37047af6d/frame95/dhdl95.xvg&amp;#x27;, &amp;#x27;fa78b971-e0cd-4f42-99d6-53c37047af6d/frame96/dhdl96.xvg&amp;#x27;, &amp;#x27;fa78b971-e0cd-4f42-99d6-53c37047af6d/frame97/dhdl97.xvg&amp;#x27;, &amp;#x27;fa78b971-e0cd-4f42-99d6-53c37047af6d/frame98/dhdl98.xvg&amp;#x27;, &amp;#x27;fa78b971-e0cd-4f42-99d6-53c37047af6d/frame99/dhdl99.xvg&amp;#x27;]\nINFO     /tmp/biobb/unitests_35/pmxanalyse/pmxanalyse_log.out:file_utils.py:172 Extracting: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/xvg_B.zip\nINFO     /tmp/biobb/unitests_35/pmxanalyse/pmxanalyse_log.out:file_utils.py:173 to:\nINFO     /tmp/biobb/unitests_35/pmxanalyse/pmxanalyse_log.out:file_utils.py:174 [&amp;#x27;7f115544-785b-40d7-ad77-b07c2aa09840/frame0/dhdl0.xvg&amp;#x27;, &amp;#x27;7f115544-785b-40d7-ad77-b07c2aa09840/frame1/dhdl1.xvg&amp;#x27;, 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&amp;#x27;7f115544-785b-40d7-ad77-b07c2aa09840/frame81/dhdl81.xvg&amp;#x27;, &amp;#x27;7f115544-785b-40d7-ad77-b07c2aa09840/frame82/dhdl82.xvg&amp;#x27;, &amp;#x27;7f115544-785b-40d7-ad77-b07c2aa09840/frame83/dhdl83.xvg&amp;#x27;, &amp;#x27;7f115544-785b-40d7-ad77-b07c2aa09840/frame84/dhdl84.xvg&amp;#x27;, &amp;#x27;7f115544-785b-40d7-ad77-b07c2aa09840/frame85/dhdl85.xvg&amp;#x27;, &amp;#x27;7f115544-785b-40d7-ad77-b07c2aa09840/frame86/dhdl86.xvg&amp;#x27;, &amp;#x27;7f115544-785b-40d7-ad77-b07c2aa09840/frame87/dhdl87.xvg&amp;#x27;, &amp;#x27;7f115544-785b-40d7-ad77-b07c2aa09840/frame88/dhdl88.xvg&amp;#x27;, &amp;#x27;7f115544-785b-40d7-ad77-b07c2aa09840/frame89/dhdl89.xvg&amp;#x27;, &amp;#x27;7f115544-785b-40d7-ad77-b07c2aa09840/frame9/dhdl9.xvg&amp;#x27;, &amp;#x27;7f115544-785b-40d7-ad77-b07c2aa09840/frame90/dhdl90.xvg&amp;#x27;, &amp;#x27;7f115544-785b-40d7-ad77-b07c2aa09840/frame91/dhdl91.xvg&amp;#x27;, &amp;#x27;7f115544-785b-40d7-ad77-b07c2aa09840/frame92/dhdl92.xvg&amp;#x27;, &amp;#x27;7f115544-785b-40d7-ad77-b07c2aa09840/frame93/dhdl93.xvg&amp;#x27;, &amp;#x27;7f115544-785b-40d7-ad77-b07c2aa09840/frame94/dhdl94.xvg&amp;#x27;, &amp;#x27;7f115544-785b-40d7-ad77-b07c2aa09840/frame95/dhdl95.xvg&amp;#x27;, &amp;#x27;7f115544-785b-40d7-ad77-b07c2aa09840/frame96/dhdl96.xvg&amp;#x27;, &amp;#x27;7f115544-785b-40d7-ad77-b07c2aa09840/frame97/dhdl97.xvg&amp;#x27;, &amp;#x27;7f115544-785b-40d7-ad77-b07c2aa09840/frame98/dhdl98.xvg&amp;#x27;, &amp;#x27;7f115544-785b-40d7-ad77-b07c2aa09840/frame99/dhdl99.xvg&amp;#x27;]\nINFO     /tmp/biobb/unitests_35/pmxanalyse/pmxanalyse_log.out:cmd_wrapper.py:63 pmx analyse -fA fa78b971-e0cd-4f42-99d6-53c37047af6d/frame0/dhdl0.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame1/dhdl1.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame10/dhdl10.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame11/dhdl11.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame12/dhdl12.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame13/dhdl13.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame14/dhdl14.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame15/dhdl15.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame16/dhdl16.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame17/dhdl17.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame18/dhdl18.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame19/dhdl19.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame2/dhdl2.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame20/dhdl20.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame21/dhdl21.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame22/dhdl22.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame23/dhdl23.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame24/dhdl24.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame25/dhdl25.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame26/dhdl26.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame27/dhdl27.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame28/dhdl28.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame29/dhdl29.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame3/dhdl3.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame30/dhdl30.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame31/dhdl31.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame32/dhdl32.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame33/dhdl33.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame34/dhdl34.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame35/dhdl35.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame36/dhdl36.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame37/dhdl37.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame38/dhdl38.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame39/dhdl39.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame4/dhdl4.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame40/dhdl40.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame41/dhdl41.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame42/dhdl42.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame43/dhdl43.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame44/dhdl44.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame45/dhdl45.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame46/dhdl46.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame47/dhdl47.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame48/dhdl48.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame49/dhdl49.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame5/dhdl5.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame50/dhdl50.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame51/dhdl51.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame52/dhdl52.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame53/dhdl53.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame54/dhdl54.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame55/dhdl55.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame56/dhdl56.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame57/dhdl57.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame58/dhdl58.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame59/dhdl59.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame6/dhdl6.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame60/dhdl60.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame61/dhdl61.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame62/dhdl62.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame63/dhdl63.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame64/dhdl64.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame65/dhdl65.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame66/dhdl66.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame67/dhdl67.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame68/dhdl68.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame69/dhdl69.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame7/dhdl7.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame70/dhdl70.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame71/dhdl71.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame72/dhdl72.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame73/dhdl73.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame74/dhdl74.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame75/dhdl75.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame76/dhdl76.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame77/dhdl77.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame78/dhdl78.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame79/dhdl79.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame8/dhdl8.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame80/dhdl80.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame81/dhdl81.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame82/dhdl82.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame83/dhdl83.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame84/dhdl84.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame85/dhdl85.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame86/dhdl86.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame87/dhdl87.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame88/dhdl88.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame89/dhdl89.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame9/dhdl9.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame90/dhdl90.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame91/dhdl91.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame92/dhdl92.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame93/dhdl93.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame94/dhdl94.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame95/dhdl95.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame96/dhdl96.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame97/dhdl97.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame98/dhdl98.xvg fa78b971-e0cd-4f42-99d6-53c37047af6d/frame99/dhdl99.xvg -fB 7f115544-785b-40d7-ad77-b07c2aa09840/frame0/dhdl0.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame1/dhdl1.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame10/dhdl10.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame11/dhdl11.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame12/dhdl12.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame13/dhdl13.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame14/dhdl14.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame15/dhdl15.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame16/dhdl16.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame17/dhdl17.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame18/dhdl18.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame19/dhdl19.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame2/dhdl2.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame20/dhdl20.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame21/dhdl21.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame22/dhdl22.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame23/dhdl23.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame24/dhdl24.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame25/dhdl25.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame26/dhdl26.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame27/dhdl27.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame28/dhdl28.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame29/dhdl29.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame3/dhdl3.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame30/dhdl30.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame31/dhdl31.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame32/dhdl32.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame33/dhdl33.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame34/dhdl34.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame35/dhdl35.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame36/dhdl36.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame37/dhdl37.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame38/dhdl38.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame39/dhdl39.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame4/dhdl4.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame40/dhdl40.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame41/dhdl41.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame42/dhdl42.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame43/dhdl43.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame44/dhdl44.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame45/dhdl45.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame46/dhdl46.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame47/dhdl47.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame48/dhdl48.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame49/dhdl49.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame5/dhdl5.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame50/dhdl50.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame51/dhdl51.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame52/dhdl52.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame53/dhdl53.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame54/dhdl54.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame55/dhdl55.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame56/dhdl56.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame57/dhdl57.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame58/dhdl58.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame59/dhdl59.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame6/dhdl6.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame60/dhdl60.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame61/dhdl61.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame62/dhdl62.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame63/dhdl63.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame64/dhdl64.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame65/dhdl65.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame66/dhdl66.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame67/dhdl67.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame68/dhdl68.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame69/dhdl69.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame7/dhdl7.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame70/dhdl70.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame71/dhdl71.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame72/dhdl72.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame73/dhdl73.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame74/dhdl74.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame75/dhdl75.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame76/dhdl76.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame77/dhdl77.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame78/dhdl78.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame79/dhdl79.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame8/dhdl8.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame80/dhdl80.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame81/dhdl81.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame82/dhdl82.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame83/dhdl83.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame84/dhdl84.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame85/dhdl85.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame86/dhdl86.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame87/dhdl87.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame88/dhdl88.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame89/dhdl89.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame9/dhdl9.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame90/dhdl90.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame91/dhdl91.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame92/dhdl92.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame93/dhdl93.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame94/dhdl94.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame95/dhdl95.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame96/dhdl96.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame97/dhdl97.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame98/dhdl98.xvg 7f115544-785b-40d7-ad77-b07c2aa09840/frame99/dhdl99.xvg -o /tmp/biobb/unitests_35/pmxanalyse/sandbox_caa2a2bb-d1c7-4712-91de-2bfa47012916/result.txt -w /tmp/biobb/unitests_35/pmxanalyse/sandbox_caa2a2bb-d1c7-4712-91de-2bfa47012916/plot.png -m CGI BAR JARZ -t 298.15 -n 1 --skip 1 --prec 2 --units kJ --nbins 20 --dpi 600\n\nINFO     /tmp/biobb/unitests_35/pmxanalyse/pmxanalyse_log.out:cmd_wrapper.py:36 Executing: pmx analyse -fA fa78b971-e0cd-4f42-99d6-53c37047af6d/frame0/dhdl0.xvg fa78b971-e...\nINFO     /tmp/biobb/unitests_35/pmxanalyse/pmxanalyse_log.out:cmd_wrapper.py:37 Exit code: 0\nINFO     /tmp/biobb/unitests_35/pmxanalyse/pmxanalyse_log.out:cmd_wrapper.py:41 \n\n ========================================================\n                   PROCESSING THE DATA\n ========================================================\n  Forward Data\n    First accepted file: fa78b971-e0cd-4f42-99d6-53c37047af6d/frame0/dhdl0.xvg\n    # data points: 25001\n    Length of trajectory:   50.000 ps\n    Delta lambda:  0.00004\n\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame1/dhdl1.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame2/dhdl2.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame3/dhdl3.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame4/dhdl4.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame5/dhdl5.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame6/dhdl6.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame7/dhdl7.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame8/dhdl8.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame9/dhdl9.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame10/dhdl10.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame11/dhdl11.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame12/dhdl12.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame13/dhdl13.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame14/dhdl14.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame15/dhdl15.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame16/dhdl16.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame17/dhdl17.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame18/dhdl18.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame19/dhdl19.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame20/dhdl20.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame21/dhdl21.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame22/dhdl22.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame23/dhdl23.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame24/dhdl24.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame25/dhdl25.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame26/dhdl26.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame27/dhdl27.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame28/dhdl28.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame29/dhdl29.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame30/dhdl30.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame31/dhdl31.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame32/dhdl32.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame33/dhdl33.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame34/dhdl34.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame35/dhdl35.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame36/dhdl36.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame37/dhdl37.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame38/dhdl38.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame39/dhdl39.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame40/dhdl40.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame41/dhdl41.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame42/dhdl42.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame43/dhdl43.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame44/dhdl44.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame45/dhdl45.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame46/dhdl46.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame47/dhdl47.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame48/dhdl48.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame49/dhdl49.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame50/dhdl50.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame51/dhdl51.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame52/dhdl52.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame53/dhdl53.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame54/dhdl54.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame55/dhdl55.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame56/dhdl56.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame57/dhdl57.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame58/dhdl58.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame59/dhdl59.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame60/dhdl60.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame61/dhdl61.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame62/dhdl62.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame63/dhdl63.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame64/dhdl64.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame65/dhdl65.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame66/dhdl66.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame67/dhdl67.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame68/dhdl68.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame69/dhdl69.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame70/dhdl70.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame71/dhdl71.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame72/dhdl72.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame73/dhdl73.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame74/dhdl74.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame75/dhdl75.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame76/dhdl76.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame77/dhdl77.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame78/dhdl78.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame79/dhdl79.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame80/dhdl80.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame81/dhdl81.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame82/dhdl82.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame83/dhdl83.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame84/dhdl84.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame85/dhdl85.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame86/dhdl86.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame87/dhdl87.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame88/dhdl88.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame89/dhdl89.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame90/dhdl90.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame91/dhdl91.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame92/dhdl92.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame93/dhdl93.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame94/dhdl94.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame95/dhdl95.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame96/dhdl96.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame97/dhdl97.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame98/dhdl98.xvg\r    Reading fa78b971-e0cd-4f42-99d6-53c37047af6d/frame99/dhdl99.xvg\n\n  Reverse Data\n    First accepted file: 7f115544-785b-40d7-ad77-b07c2aa09840/frame0/dhdl0.xvg\n    # data points: 25001\n    Length of trajectory:   50.000 ps\n    Delta lambda: -0.00004\n\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame1/dhdl1.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame2/dhdl2.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame3/dhdl3.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame4/dhdl4.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame5/dhdl5.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame6/dhdl6.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame7/dhdl7.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame8/dhdl8.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame9/dhdl9.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame10/dhdl10.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame11/dhdl11.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame12/dhdl12.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame13/dhdl13.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame14/dhdl14.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame15/dhdl15.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame16/dhdl16.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame17/dhdl17.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame18/dhdl18.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame19/dhdl19.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame20/dhdl20.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame21/dhdl21.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame22/dhdl22.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame23/dhdl23.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame24/dhdl24.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame25/dhdl25.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame26/dhdl26.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame27/dhdl27.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame28/dhdl28.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame29/dhdl29.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame30/dhdl30.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame31/dhdl31.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame32/dhdl32.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame33/dhdl33.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame34/dhdl34.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame35/dhdl35.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame36/dhdl36.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame37/dhdl37.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame38/dhdl38.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame39/dhdl39.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame40/dhdl40.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame41/dhdl41.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame42/dhdl42.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame43/dhdl43.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame44/dhdl44.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame45/dhdl45.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame46/dhdl46.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame47/dhdl47.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame48/dhdl48.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame49/dhdl49.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame50/dhdl50.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame51/dhdl51.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame52/dhdl52.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame53/dhdl53.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame54/dhdl54.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame55/dhdl55.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame56/dhdl56.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame57/dhdl57.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame58/dhdl58.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame59/dhdl59.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame60/dhdl60.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame61/dhdl61.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame62/dhdl62.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame63/dhdl63.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame64/dhdl64.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame65/dhdl65.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame66/dhdl66.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame67/dhdl67.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame68/dhdl68.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame69/dhdl69.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame70/dhdl70.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame71/dhdl71.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame72/dhdl72.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame73/dhdl73.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame74/dhdl74.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame75/dhdl75.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame76/dhdl76.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame77/dhdl77.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame78/dhdl78.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame79/dhdl79.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame80/dhdl80.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame81/dhdl81.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame82/dhdl82.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame83/dhdl83.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame84/dhdl84.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame85/dhdl85.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame86/dhdl86.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame87/dhdl87.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame88/dhdl88.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame89/dhdl89.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame90/dhdl90.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame91/dhdl91.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame92/dhdl92.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame93/dhdl93.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame94/dhdl94.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame95/dhdl95.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame96/dhdl96.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame97/dhdl97.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame98/dhdl98.xvg\r    Reading 7f115544-785b-40d7-ad77-b07c2aa09840/frame99/dhdl99.xvg\n\n ========================================================\n                       ANALYSIS\n ========================================================\n  Number of forward (0-&amp;gt;1) trajectories: 100\n  Number of reverse (1-&amp;gt;0) trajectories: 100\n  Temperature : 298.15 K\n\n --------------------------------------------------------\n             Crooks Gaussian Intersection     \n --------------------------------------------------------\n  Calculating Intersection...\n\r  Bootstrap (Std Err): iteration 1/100\r  Bootstrap (Std Err): iteration 2/100\r  Bootstrap (Std Err): iteration 3/100\r  Bootstrap (Std Err): iteration 4/100\r  Bootstrap (Std Err): iteration 5/100\r  Bootstrap (Std Err): iteration 6/100\r  Bootstrap (Std Err): iteration 7/100\r  Bootstrap (Std Err): iteration 8/100\r  Bootstrap (Std Err): iteration 9/100\r  Bootstrap (Std Err): iteration 10/100\r  Bootstrap (Std Err): iteration 11/100\r  Bootstrap (Std Err): iteration 12/100\r  Bootstrap (Std Err): iteration 13/100\r  Bootstrap (Std Err): iteration 14/100\r  Bootstrap (Std Err): iteration 15/100\r  Bootstrap (Std Err): iteration 16/100\r  Bootstrap (Std Err): iteration 17/100\r  Bootstrap (Std Err): iteration 18/100\r  Bootstrap (Std Err): iteration 19/100\r  Bootstrap (Std Err): iteration 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Err): iteration 69/100\r  Bootstrap (Std Err): iteration 70/100\r  Bootstrap (Std Err): iteration 71/100\r  Bootstrap (Std Err): iteration 72/100\r  Bootstrap (Std Err): iteration 73/100\r  Bootstrap (Std Err): iteration 74/100\r  Bootstrap (Std Err): iteration 75/100\r  Bootstrap (Std Err): iteration 76/100\r  Bootstrap (Std Err): iteration 77/100\r  Bootstrap (Std Err): iteration 78/100\r  Bootstrap (Std Err): iteration 79/100\r  Bootstrap (Std Err): iteration 80/100\r  Bootstrap (Std Err): iteration 81/100\r  Bootstrap (Std Err): iteration 82/100\r  Bootstrap (Std Err): iteration 83/100\r  Bootstrap (Std Err): iteration 84/100\r  Bootstrap (Std Err): iteration 85/100\r  Bootstrap (Std Err): iteration 86/100\r  Bootstrap (Std Err): iteration 87/100\r  Bootstrap (Std Err): iteration 88/100\r  Bootstrap (Std Err): iteration 89/100\r  Bootstrap (Std Err): iteration 90/100\r  Bootstrap (Std Err): iteration 91/100\r  Bootstrap (Std Err): iteration 92/100\r  Bootstrap (Std Err): iteration 93/100\r  Bootstrap (Std Err): iteration 94/100\r  Bootstrap (Std Err): iteration 95/100\r  Bootstrap (Std Err): iteration 96/100\r  Bootstrap (Std Err): iteration 97/100\r  Bootstrap (Std Err): iteration 98/100\r  Bootstrap (Std Err): iteration 99/100\r  Bootstrap (Std Err): iteration 100/100\n  CGI: Forward Gauss mean =    13.51 kJ/mol std =     4.03 kJ/mol\n  CGI: Reverse Gauss mean =     5.40 kJ/mol std =     8.49 kJ/mol\n  CGI: dG =     8.39 kJ/mol\n  CGI: Std Err (bootstrap:parametric) =     0.42 kJ/mol\n  CGI: Std Err (bootstrap) =     0.43 kJ/mol\n\n  Running KS-test...\n    Forward: gaussian quality = 0.41\n             ---&amp;gt; KS-Test Ok\n    Reverse: gaussian quality = 0.98\n             ---&amp;gt; KS-Test Ok\n\n --------------------------------------------------------\n             Bennett Acceptance Ratio     \n --------------------------------------------------------\n  Running Nelder-Mead Simplex algorithm... \n\r  Bootstrap (Std Err): iteration 1/100\r  Bootstrap 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99/100\r  Bootstrap (Std Err): iteration 100/100\n\r  Bootstrap (Conv): iteration 1/100\r  Bootstrap (Conv): iteration 2/100\r  Bootstrap (Conv): iteration 3/100\r  Bootstrap (Conv): iteration 4/100\r  Bootstrap (Conv): iteration 5/100\r  Bootstrap (Conv): iteration 6/100\r  Bootstrap (Conv): iteration 7/100\r  Bootstrap (Conv): iteration 8/100\r  Bootstrap (Conv): iteration 9/100\r  Bootstrap (Conv): iteration 10/100\r  Bootstrap (Conv): iteration 11/100\r  Bootstrap (Conv): iteration 12/100\r  Bootstrap (Conv): iteration 13/100\r  Bootstrap (Conv): iteration 14/100\r  Bootstrap (Conv): iteration 15/100\r  Bootstrap (Conv): iteration 16/100\r  Bootstrap (Conv): iteration 17/100\r  Bootstrap (Conv): iteration 18/100\r  Bootstrap (Conv): iteration 19/100\r  Bootstrap (Conv): iteration 20/100\r  Bootstrap (Conv): iteration 21/100\r  Bootstrap (Conv): iteration 22/100\r  Bootstrap (Conv): iteration 23/100\r  Bootstrap (Conv): iteration 24/100\r  Bootstrap (Conv): iteration 25/100\r  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-0.23\n  BAR: Conv Std Err (bootstrap) =     0.06\n\n --------------------------------------------------------\n             Jarzynski estimator     \n --------------------------------------------------------\n\r  Bootstrap (Std Err): iteration 1/100\r  Bootstrap (Std Err): iteration 2/100\r  Bootstrap (Std Err): iteration 3/100\r  Bootstrap (Std Err): iteration 4/100\r  Bootstrap (Std Err): iteration 5/100\r  Bootstrap (Std Err): iteration 6/100\r  Bootstrap (Std Err): iteration 7/100\r  Bootstrap (Std Err): iteration 8/100\r  Bootstrap (Std Err): iteration 9/100\r  Bootstrap (Std Err): iteration 10/100\r  Bootstrap (Std Err): iteration 11/100\r  Bootstrap (Std Err): iteration 12/100\r  Bootstrap (Std Err): iteration 13/100\r  Bootstrap (Std Err): iteration 14/100\r  Bootstrap (Std Err): iteration 15/100\r  Bootstrap (Std Err): iteration 16/100\r  Bootstrap (Std Err): iteration 17/100\r  Bootstrap (Std Err): iteration 18/100\r  Bootstrap (Std Err): iteration 19/100\r  Bootstrap (Std 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Bootstrap (Std Err): iteration 80/100\r  Bootstrap (Std Err): iteration 81/100\r  Bootstrap (Std Err): iteration 82/100\r  Bootstrap (Std Err): iteration 83/100\r  Bootstrap (Std Err): iteration 84/100\r  Bootstrap (Std Err): iteration 85/100\r  Bootstrap (Std Err): iteration 86/100\r  Bootstrap (Std Err): iteration 87/100\r  Bootstrap (Std Err): iteration 88/100\r  Bootstrap (Std Err): iteration 89/100\r  Bootstrap (Std Err): iteration 90/100\r  Bootstrap (Std Err): iteration 91/100\r  Bootstrap (Std Err): iteration 92/100\r  Bootstrap (Std Err): iteration 93/100\r  Bootstrap (Std Err): iteration 94/100\r  Bootstrap (Std Err): iteration 95/100\r  Bootstrap (Std Err): iteration 96/100\r  Bootstrap (Std Err): iteration 97/100\r  Bootstrap (Std Err): iteration 98/100\r  Bootstrap (Std Err): iteration 99/100\r  Bootstrap (Std Err): iteration 100/100\n  JARZ_Gauss: dG Forward =    10.19 kJ/mol\n  JARZ_Gauss: dG Reverse =    20.07 kJ/mol\n  JARZ_Gauss: dG Mean    =    15.13 kJ/mol\n  JARZ_Gauss: Std Err (analytical) Forward =     0.62 kJ/mol\n  JARZ_Gauss: Std Err (analytical) Reverse =     2.25 kJ/mol\n  JARZ_Gauss: Std Err Forward (bootstrap) =     0.64 kJ/mol\n  JARZ_Gauss: Std Err Reverse (bootstrap) =     2.45 kJ/mol\n ========================================================\n\n   Plotting histograms......\n\n   ......done...........\n\n   Execution time = 00:00:10\n\n\nINFO     /tmp/biobb/unitests_35/pmxanalyse/pmxanalyse_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_35/pmxanalyse/sandbox_caa2a2bb-d1c7-4712-91de-2bfa47012916&amp;#x27;, &amp;#x27;fa78b971-e0cd-4f42-99d6-53c37047af6d&amp;#x27;, &amp;#x27;7f115544-785b-40d7-ad77-b07c2aa09840&amp;#x27;]\nINFO     /tmp/biobb/unitests_35/pmxanalyse/pmxanalyse_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_35\n&#34;}], &#34;biobb_pmx/test/unitests/test_pmx/test_pmxatom_mapping.py::TestPmxatom_mapping::test_pmxatom_mapping&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_pmx/test/unitests/test_pmx/test_pmxatom_mapping.py::TestPmxatom_mapping::test_pmxatom_mapping&#34;, &#34;duration&#34;: &#34;00:00:05&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_pmx/test/unitests/test_pmx/test_pmxatom_mapping.py::TestPmxatom_mapping::test_pmxatom_mapping&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:00:05&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-11-04 15:33:10,327 [MainThread  ] [INFO ]  Module: biobb_pmx.pmxbiobb.pmxatom_mapping Version: 4.2.1\n2024-11-04 15:33:10,327 [MainThread  ] [INFO ]  /tmp/biobb/unitests_35/pmxatom_mapping/sandbox_549c297f-0571-4d4d-bd37-6710b748728f directory successfully created\n2024-11-04 15:33:10,328 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/lig1.pdb to /tmp/biobb/unitests_35/pmxatom_mapping/sandbox_549c297f-0571-4d4d-bd37-6710b748728f\n2024-11-04 15:33:10,328 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/lig2.pdb to /tmp/biobb/unitests_35/pmxatom_mapping/sandbox_549c297f-0571-4d4d-bd37-6710b748728f\n2024-11-04 15:33:10,328 [MainThread  ] [INFO ]  pmx atomMapping -i1 /tmp/biobb/unitests_35/pmxatom_mapping/sandbox_549c297f-0571-4d4d-bd37-6710b748728f/lig1.pdb -i2 /tmp/biobb/unitests_35/pmxatom_mapping/sandbox_549c297f-0571-4d4d-bd37-6710b748728f/lig2.pdb -o1 /tmp/biobb/unitests_35/pmxatom_mapping/sandbox_549c297f-0571-4d4d-bd37-6710b748728f/pairs1.dat -o2 /tmp/biobb/unitests_35/pmxatom_mapping/sandbox_549c297f-0571-4d4d-bd37-6710b748728f/pairs2.dat -log /tmp/biobb/unitests_35/pmxatom_mapping/sandbox_549c297f-0571-4d4d-bd37-6710b748728f/atom_mapping.log --d 0.05\n\n2024-11-04 15:33:14,930 [MainThread  ] [INFO ]  Executing: pmx atomMapping -i1 /tmp/biobb/unitests_35/pmxatom_mapping/sandbox_549c297f-0571...\n2024-11-04 15:33:14,931 [MainThread  ] [INFO ]  Exit code: 0\n2024-11-04 15:33:14,931 [MainThread  ] [INFO ]  atomMapping__log_&amp;gt; Morphable atoms will be identified using the following methods:\natomMapping__log_&amp;gt; Alignment: True\natomMapping__log_&amp;gt; MCS: True\natomMapping__log_&amp;gt; Initializing the main LigandsAtomMapping object\natomMapping__log_&amp;gt; The topology matching approach will be used (MCS)\natomMapping__log_&amp;gt; fmcs module: Copyright (c) 2012 Andrew Dalke Scientific AB\natomMapping__log_&amp;gt; MCS: trying to run an MCS using all atoms: modified molecules, match elements...\natomMapping__log_&amp;gt; MCS searching...\natomMapping__log_&amp;gt; Found 4 MCSs in total (mol1: 2, mol2: 2), each with 22 atoms and 23 bonds\natomMapping__log_&amp;gt; Chirality check.\natomMapping__log_&amp;gt; Avoiding breaking rings.\natomMapping__log_&amp;gt; Final MCS that survived after pruning: 33 atoms\natomMapping__log_&amp;gt; MCS: all atoms, modified molecules, size of mapping: 33\natomMapping__log_&amp;gt; MCS: trying to run an MCS using all atoms: unmodified molecules, match elements...\natomMapping__log_&amp;gt; MCS searching...\natomMapping__log_&amp;gt; Found 4 MCSs in total (mol1: 2, mol2: 2), each with 22 atoms and 23 bonds\natomMapping__log_&amp;gt; Chirality check.\natomMapping__log_&amp;gt; Avoiding breaking rings.\natomMapping__log_&amp;gt; Final MCS that survived after pruning: 33 atoms\natomMapping__log_&amp;gt; MCS: all atoms, unmodified molecules, size of mapping: 33\natomMapping__log_&amp;gt; MCS: trying to run an MCS using rings only...\natomMapping__log_&amp;gt; MCS searching...\natomMapping__log_&amp;gt; Found 576 MCSs in total (mol1: 24, mol2: 24), each with 6 atoms and 6 bonds\natomMapping__log_&amp;gt; Chirality check.\natomMapping__log_&amp;gt; Avoiding breaking rings.\natomMapping__log_&amp;gt; Final MCS that survived after pruning: 7 atoms\natomMapping__log_&amp;gt; MCS: using variant with the mapping size of 33\natomMapping__log_&amp;gt; The alignment approach will be used\natomMapping__log_&amp;gt; Tosco, P., Balle, T. &amp;amp; Shiri, F. Open3DALIGN: an open-source software aimed at unsupervised ligand alignment. J Comput Aided Mol Des 25:777-83 (2011)\natomMapping__log_&amp;gt; Alignment is based on atom logP contributions: S. A. Wildman and G. M. Crippen JCICS _39_ 868-873 (1999)\natomMapping__log_&amp;gt; Alignment: trying to align all atoms...\natomMapping__log_&amp;gt; Avoiding breaking rings.\natomMapping__log_&amp;gt; Alignment: size of mapping: 25\natomMapping__log_&amp;gt; Alignment: trying to align rings only...\natomMapping__log_&amp;gt; Avoiding breaking rings.\natomMapping__log_&amp;gt; Size of mapping: 31\natomMapping__log_&amp;gt; Alignment: using ring only alignment result.\natomMapping__log_&amp;gt; The final result is based on the MCS.\n\natomMapping__log_&amp;gt; Final results:\natomMapping__log_&amp;gt; Atoms considered in mol1: 39\natomMapping__log_&amp;gt; Atoms considered in mol2: 39\natomMapping__log_&amp;gt; Morphable atoms in both molecules: 33 33\natomMapping__log_&amp;gt; Dissimilarity (distance) score: 0.1538\n\n\n2024-11-04 15:33:14,932 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_35/pmxatom_mapping/sandbox_549c297f-0571-4d4d-bd37-6710b748728f&amp;#x27;]\n2024-11-04 15:33:14,932 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_35/pmxatom_mapping/pairs1.dat\nChecking if empty file: /tmp/biobb/unitests_35/pmxatom_mapping/pairs2.dat\nComparing: \n        File_A: /tmp/biobb/unitests_35/pmxatom_mapping/pairs1.dat\n        File_B: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/reference/pmx/ref_pairs1.dat\n        File_A hash: b&amp;#x27;r\\x0f\\xa3\\xb7,\\xd2D\\xcbo&amp;quot;.\\xc5o%\\x1fXD\\xce3\\xaf\\xb6\\xe4:V\\xae\\x04\\x1e\\x90Nd\\xf4\\x87&amp;#x27;\n        File_B hash: b&amp;#x27;r\\x0f\\xa3\\xb7,\\xd2D\\xcbo&amp;quot;.\\xc5o%\\x1fXD\\xce3\\xaf\\xb6\\xe4:V\\xae\\x04\\x1e\\x90Nd\\xf4\\x87&amp;#x27;\nComparing: \n        File_A: /tmp/biobb/unitests_35/pmxatom_mapping/pairs2.dat\n        File_B: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/reference/pmx/ref_pairs2.dat\n        File_A hash: b&amp;#x27;\\xc8|}\\xca\\xb4\\x1c\\x89\\xe3@W\\xd1\\xa7\\xe7\\x06\\xca\\xbb\\xae#M$6Z2\\xba\\xadXj\\x85\\xd1\\xa0\\xa8\\xad&amp;#x27;\n        File_B hash: b&amp;#x27;\\xc8|}\\xca\\xb4\\x1c\\x89\\xe3@W\\xd1\\xa7\\xe7\\x06\\xca\\xbb\\xae#M$6Z2\\xba\\xadXj\\x85\\xd1\\xa0\\xa8\\xad&amp;#x27;\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_35/pmxatom_mapping/pmxatom_mapping_log.out:file_utils.py:409 Module: biobb_pmx.pmxbiobb.pmxatom_mapping Version: 4.2.1\nINFO     /tmp/biobb/unitests_35/pmxatom_mapping/pmxatom_mapping_log.out:file_utils.py:82 /tmp/biobb/unitests_35/pmxatom_mapping/sandbox_549c297f-0571-4d4d-bd37-6710b748728f directory successfully created\nINFO     /tmp/biobb/unitests_35/pmxatom_mapping/pmxatom_mapping_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/lig1.pdb to /tmp/biobb/unitests_35/pmxatom_mapping/sandbox_549c297f-0571-4d4d-bd37-6710b748728f\nINFO     /tmp/biobb/unitests_35/pmxatom_mapping/pmxatom_mapping_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/lig2.pdb to /tmp/biobb/unitests_35/pmxatom_mapping/sandbox_549c297f-0571-4d4d-bd37-6710b748728f\nINFO     /tmp/biobb/unitests_35/pmxatom_mapping/pmxatom_mapping_log.out:cmd_wrapper.py:63 pmx atomMapping -i1 /tmp/biobb/unitests_35/pmxatom_mapping/sandbox_549c297f-0571-4d4d-bd37-6710b748728f/lig1.pdb -i2 /tmp/biobb/unitests_35/pmxatom_mapping/sandbox_549c297f-0571-4d4d-bd37-6710b748728f/lig2.pdb -o1 /tmp/biobb/unitests_35/pmxatom_mapping/sandbox_549c297f-0571-4d4d-bd37-6710b748728f/pairs1.dat -o2 /tmp/biobb/unitests_35/pmxatom_mapping/sandbox_549c297f-0571-4d4d-bd37-6710b748728f/pairs2.dat -log /tmp/biobb/unitests_35/pmxatom_mapping/sandbox_549c297f-0571-4d4d-bd37-6710b748728f/atom_mapping.log --d 0.05\n\nINFO     /tmp/biobb/unitests_35/pmxatom_mapping/pmxatom_mapping_log.out:cmd_wrapper.py:36 Executing: pmx atomMapping -i1 /tmp/biobb/unitests_35/pmxatom_mapping/sandbox_549c297f-0571...\nINFO     /tmp/biobb/unitests_35/pmxatom_mapping/pmxatom_mapping_log.out:cmd_wrapper.py:37 Exit code: 0\nINFO     /tmp/biobb/unitests_35/pmxatom_mapping/pmxatom_mapping_log.out:cmd_wrapper.py:41 atomMapping__log_&amp;gt; Morphable atoms will be identified using the following methods:\natomMapping__log_&amp;gt; Alignment: True\natomMapping__log_&amp;gt; MCS: True\natomMapping__log_&amp;gt; Initializing the main LigandsAtomMapping object\natomMapping__log_&amp;gt; The topology matching approach will be used (MCS)\natomMapping__log_&amp;gt; fmcs module: Copyright (c) 2012 Andrew Dalke Scientific AB\natomMapping__log_&amp;gt; MCS: trying to run an MCS using all atoms: modified molecules, match elements...\natomMapping__log_&amp;gt; MCS searching...\natomMapping__log_&amp;gt; Found 4 MCSs in total (mol1: 2, mol2: 2), each with 22 atoms and 23 bonds\natomMapping__log_&amp;gt; Chirality check.\natomMapping__log_&amp;gt; Avoiding breaking rings.\natomMapping__log_&amp;gt; Final MCS that survived after pruning: 33 atoms\natomMapping__log_&amp;gt; MCS: all atoms, modified molecules, size of mapping: 33\natomMapping__log_&amp;gt; MCS: trying to run an MCS using all atoms: unmodified molecules, match elements...\natomMapping__log_&amp;gt; MCS searching...\natomMapping__log_&amp;gt; Found 4 MCSs in total (mol1: 2, mol2: 2), each with 22 atoms and 23 bonds\natomMapping__log_&amp;gt; Chirality check.\natomMapping__log_&amp;gt; Avoiding breaking rings.\natomMapping__log_&amp;gt; Final MCS that survived after pruning: 33 atoms\natomMapping__log_&amp;gt; MCS: all atoms, unmodified molecules, size of mapping: 33\natomMapping__log_&amp;gt; MCS: trying to run an MCS using rings only...\natomMapping__log_&amp;gt; MCS searching...\natomMapping__log_&amp;gt; Found 576 MCSs in total (mol1: 24, mol2: 24), each with 6 atoms and 6 bonds\natomMapping__log_&amp;gt; Chirality check.\natomMapping__log_&amp;gt; Avoiding breaking rings.\natomMapping__log_&amp;gt; Final MCS that survived after pruning: 7 atoms\natomMapping__log_&amp;gt; MCS: using variant with the mapping size of 33\natomMapping__log_&amp;gt; The alignment approach will be used\natomMapping__log_&amp;gt; Tosco, P., Balle, T. &amp;amp; Shiri, F. Open3DALIGN: an open-source software aimed at unsupervised ligand alignment. J Comput Aided Mol Des 25:777-83 (2011)\natomMapping__log_&amp;gt; Alignment is based on atom logP contributions: S. A. Wildman and G. M. Crippen JCICS _39_ 868-873 (1999)\natomMapping__log_&amp;gt; Alignment: trying to align all atoms...\natomMapping__log_&amp;gt; Avoiding breaking rings.\natomMapping__log_&amp;gt; Alignment: size of mapping: 25\natomMapping__log_&amp;gt; Alignment: trying to align rings only...\natomMapping__log_&amp;gt; Avoiding breaking rings.\natomMapping__log_&amp;gt; Size of mapping: 31\natomMapping__log_&amp;gt; Alignment: using ring only alignment result.\natomMapping__log_&amp;gt; The final result is based on the MCS.\n\natomMapping__log_&amp;gt; Final results:\natomMapping__log_&amp;gt; Atoms considered in mol1: 39\natomMapping__log_&amp;gt; Atoms considered in mol2: 39\natomMapping__log_&amp;gt; Morphable atoms in both molecules: 33 33\natomMapping__log_&amp;gt; Dissimilarity (distance) score: 0.1538\n\n\nINFO     /tmp/biobb/unitests_35/pmxatom_mapping/pmxatom_mapping_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_35/pmxatom_mapping/sandbox_549c297f-0571-4d4d-bd37-6710b748728f&amp;#x27;]\nINFO     /tmp/biobb/unitests_35/pmxatom_mapping/pmxatom_mapping_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_35\n&#34;}], &#34;biobb_pmx/test/unitests/test_pmx/test_pmxcreate_top.py::TestPmxcreate_top::test_pmxcreate_top&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_pmx/test/unitests/test_pmx/test_pmxcreate_top.py::TestPmxcreate_top::test_pmxcreate_top&#34;, &#34;duration&#34;: &#34;46 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_pmx/test/unitests/test_pmx/test_pmxcreate_top.py::TestPmxcreate_top::test_pmxcreate_top&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;46 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-11-04 15:33:14,968 [MainThread  ] [INFO ]  Module: biobb_pmx.pmxbiobb.pmxcreate_top Version: 4.2.1\n2024-11-04 15:33:14,968 [MainThread  ] [INFO ]  /tmp/biobb/unitests_35/pmxcreate_top/sandbox_13a4e025-982b-4f37-90ff-30d3e5606af0 directory successfully created\n2024-11-04 15:33:14,968 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/topo1.itp to /tmp/biobb/unitests_35/pmxcreate_top/sandbox_13a4e025-982b-4f37-90ff-30d3e5606af0\n2024-11-04 15:33:14,969 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/topo2.itp to /tmp/biobb/unitests_35/pmxcreate_top/sandbox_13a4e025-982b-4f37-90ff-30d3e5606af0\n2024-11-04 15:33:14,969 [MainThread  ] [INFO ]  Running create_top from pmx package...\n\n2024-11-04 15:33:14,969 [MainThread  ] [INFO ]  Creating 8957fb41-9439-4a16-bacf-153f0bdc77c0 temporary folder\n2024-11-04 15:33:14,969 [MainThread  ] [INFO ]  Creating topo1.itp itp file in temporary folder\n2024-11-04 15:33:14,969 [MainThread  ] [INFO ]  Creating topo2.itp itp file in temporary folder\n2024-11-04 15:33:14,970 [MainThread  ] [INFO ]  Compressing topology to: /tmp/biobb/unitests_35/pmxcreate_top/topo.zip\n2024-11-04 15:33:14,970 [MainThread  ] [INFO ]  Ignored file amber99sb-star-ildn-mut.ff/forcefield.itp\n2024-11-04 15:33:14,971 [MainThread  ] [INFO ]  Ignored file amber99sb-star-ildn-mut.ff/spce.itp\n2024-11-04 15:33:14,971 [MainThread  ] [INFO ]  Ignored file amber99sb-star-ildn-mut.ff/ions.itp\n2024-11-04 15:33:14,971 [MainThread  ] [INFO ]  Adding:\n2024-11-04 15:33:14,972 [MainThread  ] [INFO ]  [&amp;#x27;topo1.itp&amp;#x27;, &amp;#x27;topo2.itp&amp;#x27;, &amp;#x27;topology.top&amp;#x27;]\n2024-11-04 15:33:14,972 [MainThread  ] [INFO ]  to: /tmp/biobb/unitests_35/pmxcreate_top/topo.zip\n2024-11-04 15:33:14,972 [MainThread  ] [INFO ]  Removed: [&amp;#x27;topo1.itp&amp;#x27;, &amp;#x27;topo2.itp&amp;#x27;, &amp;#x27;topology.top&amp;#x27;]\n2024-11-04 15:33:14,972 [MainThread  ] [INFO ]  Exit code 0\n\n2024-11-04 15:33:14,972 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_35/pmxcreate_top/sandbox_13a4e025-982b-4f37-90ff-30d3e5606af0&amp;#x27;]\n2024-11-04 15:33:14,973 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_35/pmxcreate_top/topo.zip\nThis is a ZIP comparison!\nUnzipping:\nCreating a unique_dir for: /tmp/biobb/unitests_35/pmxcreate_top/topo.zip\nCreating a unique_dir for: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/reference/pmx/ref_hybridTopo.zip\nComparing TOP/ITP:\n     FILE_A: edd43e7f-d889-430e-ae63-5ff7939f3c6f/topo1.itp\n     FILE_B: 0c22ff59-cb5b-4c1b-b6a7-12747a22eb44/topo1.itp\nComparing TOP/ITP:\n     FILE_A: edd43e7f-d889-430e-ae63-5ff7939f3c6f/topo2.itp\n     FILE_B: 0c22ff59-cb5b-4c1b-b6a7-12747a22eb44/topo2.itp\nComparing TOP/ITP:\n     FILE_A: edd43e7f-d889-430e-ae63-5ff7939f3c6f/topology.top\n     FILE_B: 0c22ff59-cb5b-4c1b-b6a7-12747a22eb44/topology.top\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_35/pmxcreate_top/pmxcreate_top_log.out:file_utils.py:409 Module: biobb_pmx.pmxbiobb.pmxcreate_top Version: 4.2.1\nINFO     /tmp/biobb/unitests_35/pmxcreate_top/pmxcreate_top_log.out:file_utils.py:82 /tmp/biobb/unitests_35/pmxcreate_top/sandbox_13a4e025-982b-4f37-90ff-30d3e5606af0 directory successfully created\nINFO     /tmp/biobb/unitests_35/pmxcreate_top/pmxcreate_top_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/topo1.itp to /tmp/biobb/unitests_35/pmxcreate_top/sandbox_13a4e025-982b-4f37-90ff-30d3e5606af0\nINFO     /tmp/biobb/unitests_35/pmxcreate_top/pmxcreate_top_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/topo2.itp to /tmp/biobb/unitests_35/pmxcreate_top/sandbox_13a4e025-982b-4f37-90ff-30d3e5606af0\nINFO     /tmp/biobb/unitests_35/pmxcreate_top/pmxcreate_top_log.out:file_utils.py:409 Running create_top from pmx package...\n\nINFO     /tmp/biobb/unitests_35/pmxcreate_top/pmxcreate_top_log.out:file_utils.py:409 Creating 8957fb41-9439-4a16-bacf-153f0bdc77c0 temporary folder\nINFO     /tmp/biobb/unitests_35/pmxcreate_top/pmxcreate_top_log.out:file_utils.py:409 Creating topo1.itp itp file in temporary folder\nINFO     /tmp/biobb/unitests_35/pmxcreate_top/pmxcreate_top_log.out:file_utils.py:409 Creating topo2.itp itp file in temporary folder\nINFO     /tmp/biobb/unitests_35/pmxcreate_top/pmxcreate_top_log.out:file_utils.py:409 Compressing topology to: /tmp/biobb/unitests_35/pmxcreate_top/topo.zip\nINFO     /tmp/biobb/unitests_35/pmxcreate_top/pmxcreate_top_log.out:file_utils.py:203 Ignored file amber99sb-star-ildn-mut.ff/forcefield.itp\nINFO     /tmp/biobb/unitests_35/pmxcreate_top/pmxcreate_top_log.out:file_utils.py:203 Ignored file amber99sb-star-ildn-mut.ff/spce.itp\nINFO     /tmp/biobb/unitests_35/pmxcreate_top/pmxcreate_top_log.out:file_utils.py:203 Ignored file amber99sb-star-ildn-mut.ff/ions.itp\nINFO     /tmp/biobb/unitests_35/pmxcreate_top/pmxcreate_top_log.out:file_utils.py:148 Adding:\nINFO     /tmp/biobb/unitests_35/pmxcreate_top/pmxcreate_top_log.out:file_utils.py:149 [&amp;#x27;topo1.itp&amp;#x27;, &amp;#x27;topo2.itp&amp;#x27;, &amp;#x27;topology.top&amp;#x27;]\nINFO     /tmp/biobb/unitests_35/pmxcreate_top/pmxcreate_top_log.out:file_utils.py:150 to: /tmp/biobb/unitests_35/pmxcreate_top/topo.zip\nINFO     /tmp/biobb/unitests_35/pmxcreate_top/pmxcreate_top_log.out:file_utils.py:409 Removed: [&amp;#x27;topo1.itp&amp;#x27;, &amp;#x27;topo2.itp&amp;#x27;, &amp;#x27;topology.top&amp;#x27;]\nINFO     /tmp/biobb/unitests_35/pmxcreate_top/pmxcreate_top_log.out:file_utils.py:409 Exit code 0\n\nINFO     /tmp/biobb/unitests_35/pmxcreate_top/pmxcreate_top_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_35/pmxcreate_top/sandbox_13a4e025-982b-4f37-90ff-30d3e5606af0&amp;#x27;]\nINFO     /tmp/biobb/unitests_35/pmxcreate_top/pmxcreate_top_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_35\n&#34;}], &#34;biobb_pmx/test/unitests/test_pmx/test_pmxgentop.py::TestPmxgentop::test_pmxgentop&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_pmx/test/unitests/test_pmx/test_pmxgentop.py::TestPmxgentop::test_pmxgentop&#34;, &#34;duration&#34;: &#34;00:00:07&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_pmx/test/unitests/test_pmx/test_pmxgentop.py::TestPmxgentop::test_pmxgentop&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:00:07&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-11-04 15:33:15,013 [MainThread  ] [INFO ]  Module: biobb_pmx.pmxbiobb.pmxgentop Version: 4.2.1\n2024-11-04 15:33:15,013 [MainThread  ] [INFO ]  /tmp/biobb/unitests_35/pmxgentop/sandbox_18b1dd45-e724-4acf-a6b0-9e06a5a4f05e directory successfully created\n2024-11-04 15:33:15,015 [MainThread  ] [INFO ]  Extracting: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/mut_gmx.top.zip\n2024-11-04 15:33:15,016 [MainThread  ] [INFO ]  to:\n2024-11-04 15:33:15,016 [MainThread  ] [INFO ]  [&amp;#x27;2564ee00-21fa-4f6e-a008-af4a75176aed/p2g.top&amp;#x27;, &amp;#x27;2564ee00-21fa-4f6e-a008-af4a75176aed/p2g_Ion.itp&amp;#x27;, &amp;#x27;2564ee00-21fa-4f6e-a008-af4a75176aed/p2g_Protein_chain_A.itp&amp;#x27;, &amp;#x27;2564ee00-21fa-4f6e-a008-af4a75176aed/posre_Ion.itp&amp;#x27;, &amp;#x27;2564ee00-21fa-4f6e-a008-af4a75176aed/posre_Protein_chain_A.itp&amp;#x27;]\n2024-11-04 15:33:15,016 [MainThread  ] [INFO ]  Unzipping: \n2024-11-04 15:33:15,016 [MainThread  ] [INFO ]  /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/mut_gmx.top.zip\n2024-11-04 15:33:15,016 [MainThread  ] [INFO ]  To: \n2024-11-04 15:33:15,016 [MainThread  ] [INFO ]  2564ee00-21fa-4f6e-a008-af4a75176aed/p2g.top\n2024-11-04 15:33:15,016 [MainThread  ] [INFO ]  2564ee00-21fa-4f6e-a008-af4a75176aed/p2g_Ion.itp\n2024-11-04 15:33:15,016 [MainThread  ] [INFO ]  2564ee00-21fa-4f6e-a008-af4a75176aed/p2g_Protein_chain_A.itp\n2024-11-04 15:33:15,016 [MainThread  ] [INFO ]  2564ee00-21fa-4f6e-a008-af4a75176aed/posre_Ion.itp\n2024-11-04 15:33:15,016 [MainThread  ] [INFO ]  2564ee00-21fa-4f6e-a008-af4a75176aed/posre_Protein_chain_A.itp\n2024-11-04 15:33:15,016 [MainThread  ] [INFO ]  unique_dir_output_file: c1103f63-e595-4858-8aca-c3b2a639c72a/pmxgentop_p2g.top\n2024-11-04 15:33:15,017 [MainThread  ] [INFO ]  pmx gentop -o c1103f63-e595-4858-8aca-c3b2a639c72a/pmxgentop_p2g.top -ff amber99sb-star-ildn-mut -p 2564ee00-21fa-4f6e-a008-af4a75176aed/p2g.top\n\n2024-11-04 15:33:22,019 [MainThread  ] [INFO ]  Executing: pmx gentop -o c1103f63-e595-4858-8aca-c3b2a639c72a/pmxgentop_p2g.top -ff amber99...\n2024-11-04 15:33:22,112 [MainThread  ] [INFO ]  Exit code: 0\n2024-11-04 15:33:22,112 [MainThread  ] [INFO ]  \nlog_&amp;gt; Reading input top file &amp;quot;2564ee00-21fa-4f6e-a008-af4a75176aed/p2g.top&amp;quot;\nlog_&amp;gt; Making bonds for state B -&amp;gt; 0 bonds with perturbed atoms\nlog_&amp;gt; Making angles for state B -&amp;gt; 0 angles with perturbed atoms\nlog_&amp;gt; Making dihedrals for state B -&amp;gt; 0 dihedrals with perturbed atoms\nlog_&amp;gt; Removed 0 fake dihedrals\nlog_&amp;gt; Total charge of state A = 0\nlog_&amp;gt; Total charge of state B = 0\n\nlog_&amp;gt; Reading input itp file &amp;quot;p2g_Protein_chain_A.itp&amp;quot;&amp;quot;\nlog_&amp;gt; Scanning database for I2A \nlog_&amp;gt; Hybrid Residue -&amp;gt; 10 | I2A \nlog_&amp;gt; Making bonds for state B -&amp;gt; 22 bonds with perturbed atoms\nlog_&amp;gt; Making angles for state B -&amp;gt; 49 angles with perturbed atoms\nlog_&amp;gt; Making dihedrals for state B -&amp;gt; 57 dihedrals with perturbed atoms\nlog_&amp;gt; Removed 12 fake dihedrals\nlog_&amp;gt; Total charge of state A = 10\nlog_&amp;gt; Total charge of state B = 10\n\nlog_&amp;gt; Reading input itp file &amp;quot;p2g_Ion.itp&amp;quot;&amp;quot;\nlog_&amp;gt; Making bonds for state B -&amp;gt; 0 bonds with perturbed atoms\nlog_&amp;gt; Making angles for state B -&amp;gt; 0 angles with perturbed atoms\nlog_&amp;gt; Making dihedrals for state B -&amp;gt; 0 dihedrals with perturbed atoms\nlog_&amp;gt; Removed 0 fake dihedrals\nlog_&amp;gt; Total charge of state A = -10\nlog_&amp;gt; Total charge of state B = -10\n\nlog_&amp;gt; Writing itp file &amp;quot;/tmp/biobb/unitests_35/pmxgentop/c1103f63-e595-4858-8aca-c3b2a639c72a/pmx_p2g_Protein_chain_A.itp&amp;quot;&amp;quot;\n\nlog_&amp;gt; Writing itp file &amp;quot;/tmp/biobb/unitests_35/pmxgentop/c1103f63-e595-4858-8aca-c3b2a639c72a/pmx_p2g_Ion.itp&amp;quot;&amp;quot;\n\nlog_&amp;gt; Writing topology file &amp;quot;c1103f63-e595-4858-8aca-c3b2a639c72a/pmxgentop_p2g.top&amp;quot;&amp;quot;\n\nb-states filled...........\n\n\n2024-11-04 15:33:22,113 [MainThread  ] [INFO ]  Check if c1103f63-e595-4858-8aca-c3b2a639c72a/p2g_Protein_chain_A.itp exists\n2024-11-04 15:33:22,114 [MainThread  ] [INFO ]  Copying 2564ee00-21fa-4f6e-a008-af4a75176aed/p2g_Protein_chain_A.itp to: c1103f63-e595-4858-8aca-c3b2a639c72a\n2024-11-04 15:33:22,114 [MainThread  ] [INFO ]  Check if c1103f63-e595-4858-8aca-c3b2a639c72a/p2g_Ion.itp exists\n2024-11-04 15:33:22,114 [MainThread  ] [INFO ]  Copying 2564ee00-21fa-4f6e-a008-af4a75176aed/p2g_Ion.itp to: c1103f63-e595-4858-8aca-c3b2a639c72a\n2024-11-04 15:33:22,114 [MainThread  ] [INFO ]  Check if c1103f63-e595-4858-8aca-c3b2a639c72a/p2g.top exists\n2024-11-04 15:33:22,115 [MainThread  ] [INFO ]  Copying 2564ee00-21fa-4f6e-a008-af4a75176aed/p2g.top to: c1103f63-e595-4858-8aca-c3b2a639c72a\n2024-11-04 15:33:22,115 [MainThread  ] [INFO ]  Check if c1103f63-e595-4858-8aca-c3b2a639c72a/posre_Protein_chain_A.itp exists\n2024-11-04 15:33:22,115 [MainThread  ] [INFO ]  Copying 2564ee00-21fa-4f6e-a008-af4a75176aed/posre_Protein_chain_A.itp to: c1103f63-e595-4858-8aca-c3b2a639c72a\n2024-11-04 15:33:22,115 [MainThread  ] [INFO ]  Check if c1103f63-e595-4858-8aca-c3b2a639c72a/posre_Ion.itp exists\n2024-11-04 15:33:22,115 [MainThread  ] [INFO ]  Copying 2564ee00-21fa-4f6e-a008-af4a75176aed/posre_Ion.itp to: c1103f63-e595-4858-8aca-c3b2a639c72a\n2024-11-04 15:33:22,116 [MainThread  ] [INFO ]  Compressing topology to: /tmp/biobb/unitests_35/pmxgentop/output_topology.zip\n2024-11-04 15:33:22,116 [MainThread  ] [INFO ]  Ignored file c1103f63-e595-4858-8aca-c3b2a639c72a/amber99sb-star-ildn-mut.ff/forcefield.itp\n2024-11-04 15:33:22,126 [MainThread  ] [INFO ]  Ignored file c1103f63-e595-4858-8aca-c3b2a639c72a/amber99sb-star-ildn-mut.ff/spce.itp\n2024-11-04 15:33:22,126 [MainThread  ] [INFO ]  Ignored file c1103f63-e595-4858-8aca-c3b2a639c72a/amber99sb-star-ildn-mut.ff/ions.itp\n2024-11-04 15:33:22,129 [MainThread  ] [INFO ]  Adding:\n2024-11-04 15:33:22,129 [MainThread  ] [INFO ]  [&amp;#x27;c1103f63-e595-4858-8aca-c3b2a639c72a/pmx_p2g_Ion.itp&amp;#x27;, &amp;#x27;c1103f63-e595-4858-8aca-c3b2a639c72a/pmx_p2g_Protein_chain_A.itp&amp;#x27;, &amp;#x27;c1103f63-e595-4858-8aca-c3b2a639c72a/pmxgentop_p2g.top&amp;#x27;, &amp;#x27;c1103f63-e595-4858-8aca-c3b2a639c72a/posre_Ion.itp&amp;#x27;, &amp;#x27;c1103f63-e595-4858-8aca-c3b2a639c72a/posre_Protein_chain_A.itp&amp;#x27;]\n2024-11-04 15:33:22,129 [MainThread  ] [INFO ]  to: /tmp/biobb/unitests_35/pmxgentop/output_topology.zip\n2024-11-04 15:33:22,140 [MainThread  ] [INFO ]  Removed: [&amp;#x27;c1103f63-e595-4858-8aca-c3b2a639c72a/posre_Protein_chain_A.itp&amp;#x27;, &amp;#x27;c1103f63-e595-4858-8aca-c3b2a639c72a/pmx_p2g_Protein_chain_A.itp&amp;#x27;, &amp;#x27;c1103f63-e595-4858-8aca-c3b2a639c72a/posre_Ion.itp&amp;#x27;, &amp;#x27;c1103f63-e595-4858-8aca-c3b2a639c72a/pmx_p2g_Ion.itp&amp;#x27;, &amp;#x27;c1103f63-e595-4858-8aca-c3b2a639c72a/pmxgentop_p2g.top&amp;#x27;]\n2024-11-04 15:33:22,140 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_35/pmxgentop/output_topology.zip\nThis is a ZIP comparison!\nUnzipping:\nCreating a unique_dir for: /tmp/biobb/unitests_35/pmxgentop/output_topology.zip\nCreating a unique_dir for: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/reference/pmx/ref_mut_gmx_hybrid_top.zip\nComparing TOP/ITP:\n     FILE_A: 8c5329fe-e898-49e2-bf9c-a3b4e70e0ef1/pmx_p2g_Ion.itp\n     FILE_B: 8b905478-2970-4067-b7dc-b99838b01237/pmx_p2g_Ion.itp\nComparing TOP/ITP:\n     FILE_A: 8c5329fe-e898-49e2-bf9c-a3b4e70e0ef1/pmx_p2g_Protein_chain_A.itp\n     FILE_B: 8b905478-2970-4067-b7dc-b99838b01237/pmx_p2g_Protein_chain_A.itp\nComparing TOP/ITP:\n     FILE_A: 8c5329fe-e898-49e2-bf9c-a3b4e70e0ef1/pmxgentop_p2g.top\n     FILE_B: 8b905478-2970-4067-b7dc-b99838b01237/pmxgentop_p2g.top\nComparing TOP/ITP:\n     FILE_A: 8c5329fe-e898-49e2-bf9c-a3b4e70e0ef1/posre_Ion.itp\n     FILE_B: 8b905478-2970-4067-b7dc-b99838b01237/posre_Ion.itp\nComparing TOP/ITP:\n     FILE_A: 8c5329fe-e898-49e2-bf9c-a3b4e70e0ef1/posre_Protein_chain_A.itp\n     FILE_B: 8b905478-2970-4067-b7dc-b99838b01237/posre_Protein_chain_A.itp\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_35/pmxgentop/pmxgentop_log.out:file_utils.py:409 Module: biobb_pmx.pmxbiobb.pmxgentop Version: 4.2.1\nINFO     /tmp/biobb/unitests_35/pmxgentop/pmxgentop_log.out:file_utils.py:82 /tmp/biobb/unitests_35/pmxgentop/sandbox_18b1dd45-e724-4acf-a6b0-9e06a5a4f05e directory successfully created\nINFO     /tmp/biobb/unitests_35/pmxgentop/pmxgentop_log.out:file_utils.py:172 Extracting: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/mut_gmx.top.zip\nINFO     /tmp/biobb/unitests_35/pmxgentop/pmxgentop_log.out:file_utils.py:173 to:\nINFO     /tmp/biobb/unitests_35/pmxgentop/pmxgentop_log.out:file_utils.py:174 [&amp;#x27;2564ee00-21fa-4f6e-a008-af4a75176aed/p2g.top&amp;#x27;, &amp;#x27;2564ee00-21fa-4f6e-a008-af4a75176aed/p2g_Ion.itp&amp;#x27;, &amp;#x27;2564ee00-21fa-4f6e-a008-af4a75176aed/p2g_Protein_chain_A.itp&amp;#x27;, &amp;#x27;2564ee00-21fa-4f6e-a008-af4a75176aed/posre_Ion.itp&amp;#x27;, &amp;#x27;2564ee00-21fa-4f6e-a008-af4a75176aed/posre_Protein_chain_A.itp&amp;#x27;]\nINFO     /tmp/biobb/unitests_35/pmxgentop/pmxgentop_log.out:file_utils.py:252 Unzipping: \nINFO     /tmp/biobb/unitests_35/pmxgentop/pmxgentop_log.out:file_utils.py:253 /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/mut_gmx.top.zip\nINFO     /tmp/biobb/unitests_35/pmxgentop/pmxgentop_log.out:file_utils.py:254 To: \nINFO     /tmp/biobb/unitests_35/pmxgentop/pmxgentop_log.out:file_utils.py:256 2564ee00-21fa-4f6e-a008-af4a75176aed/p2g.top\nINFO     /tmp/biobb/unitests_35/pmxgentop/pmxgentop_log.out:file_utils.py:256 2564ee00-21fa-4f6e-a008-af4a75176aed/p2g_Ion.itp\nINFO     /tmp/biobb/unitests_35/pmxgentop/pmxgentop_log.out:file_utils.py:256 2564ee00-21fa-4f6e-a008-af4a75176aed/p2g_Protein_chain_A.itp\nINFO     /tmp/biobb/unitests_35/pmxgentop/pmxgentop_log.out:file_utils.py:256 2564ee00-21fa-4f6e-a008-af4a75176aed/posre_Ion.itp\nINFO     /tmp/biobb/unitests_35/pmxgentop/pmxgentop_log.out:file_utils.py:256 2564ee00-21fa-4f6e-a008-af4a75176aed/posre_Protein_chain_A.itp\nINFO     /tmp/biobb/unitests_35/pmxgentop/pmxgentop_log.out:file_utils.py:409 unique_dir_output_file: c1103f63-e595-4858-8aca-c3b2a639c72a/pmxgentop_p2g.top\nINFO     /tmp/biobb/unitests_35/pmxgentop/pmxgentop_log.out:cmd_wrapper.py:63 pmx gentop -o c1103f63-e595-4858-8aca-c3b2a639c72a/pmxgentop_p2g.top -ff amber99sb-star-ildn-mut -p 2564ee00-21fa-4f6e-a008-af4a75176aed/p2g.top\n\nINFO     /tmp/biobb/unitests_35/pmxgentop/pmxgentop_log.out:cmd_wrapper.py:36 Executing: pmx gentop -o c1103f63-e595-4858-8aca-c3b2a639c72a/pmxgentop_p2g.top -ff amber99...\nINFO     /tmp/biobb/unitests_35/pmxgentop/pmxgentop_log.out:cmd_wrapper.py:37 Exit code: 0\nINFO     /tmp/biobb/unitests_35/pmxgentop/pmxgentop_log.out:cmd_wrapper.py:41 \nlog_&amp;gt; Reading input top file &amp;quot;2564ee00-21fa-4f6e-a008-af4a75176aed/p2g.top&amp;quot;\nlog_&amp;gt; Making bonds for state B -&amp;gt; 0 bonds with perturbed atoms\nlog_&amp;gt; Making angles for state B -&amp;gt; 0 angles with perturbed atoms\nlog_&amp;gt; Making dihedrals for state B -&amp;gt; 0 dihedrals with perturbed atoms\nlog_&amp;gt; Removed 0 fake dihedrals\nlog_&amp;gt; Total charge of state A = 0\nlog_&amp;gt; Total charge of state B = 0\n\nlog_&amp;gt; Reading input itp file &amp;quot;p2g_Protein_chain_A.itp&amp;quot;&amp;quot;\nlog_&amp;gt; Scanning database for I2A \nlog_&amp;gt; Hybrid Residue -&amp;gt; 10 | I2A \nlog_&amp;gt; Making bonds for state B -&amp;gt; 22 bonds with perturbed atoms\nlog_&amp;gt; Making angles for state B -&amp;gt; 49 angles with perturbed atoms\nlog_&amp;gt; Making dihedrals for state B -&amp;gt; 57 dihedrals with perturbed atoms\nlog_&amp;gt; Removed 12 fake dihedrals\nlog_&amp;gt; Total charge of state A = 10\nlog_&amp;gt; Total charge of state B = 10\n\nlog_&amp;gt; Reading input itp file &amp;quot;p2g_Ion.itp&amp;quot;&amp;quot;\nlog_&amp;gt; Making bonds for state B -&amp;gt; 0 bonds with perturbed atoms\nlog_&amp;gt; Making angles for state B -&amp;gt; 0 angles with perturbed atoms\nlog_&amp;gt; Making dihedrals for state B -&amp;gt; 0 dihedrals with perturbed atoms\nlog_&amp;gt; Removed 0 fake dihedrals\nlog_&amp;gt; Total charge of state A = -10\nlog_&amp;gt; Total charge of state B = -10\n\nlog_&amp;gt; Writing itp file &amp;quot;/tmp/biobb/unitests_35/pmxgentop/c1103f63-e595-4858-8aca-c3b2a639c72a/pmx_p2g_Protein_chain_A.itp&amp;quot;&amp;quot;\n\nlog_&amp;gt; Writing itp file &amp;quot;/tmp/biobb/unitests_35/pmxgentop/c1103f63-e595-4858-8aca-c3b2a639c72a/pmx_p2g_Ion.itp&amp;quot;&amp;quot;\n\nlog_&amp;gt; Writing topology file &amp;quot;c1103f63-e595-4858-8aca-c3b2a639c72a/pmxgentop_p2g.top&amp;quot;&amp;quot;\n\nb-states filled...........\n\n\nINFO     /tmp/biobb/unitests_35/pmxgentop/pmxgentop_log.out:file_utils.py:409 Check if c1103f63-e595-4858-8aca-c3b2a639c72a/p2g_Protein_chain_A.itp exists\nINFO     /tmp/biobb/unitests_35/pmxgentop/pmxgentop_log.out:file_utils.py:409 Copying 2564ee00-21fa-4f6e-a008-af4a75176aed/p2g_Protein_chain_A.itp to: c1103f63-e595-4858-8aca-c3b2a639c72a\nINFO     /tmp/biobb/unitests_35/pmxgentop/pmxgentop_log.out:file_utils.py:409 Check if c1103f63-e595-4858-8aca-c3b2a639c72a/p2g_Ion.itp exists\nINFO     /tmp/biobb/unitests_35/pmxgentop/pmxgentop_log.out:file_utils.py:409 Copying 2564ee00-21fa-4f6e-a008-af4a75176aed/p2g_Ion.itp to: c1103f63-e595-4858-8aca-c3b2a639c72a\nINFO     /tmp/biobb/unitests_35/pmxgentop/pmxgentop_log.out:file_utils.py:409 Check if c1103f63-e595-4858-8aca-c3b2a639c72a/p2g.top exists\nINFO     /tmp/biobb/unitests_35/pmxgentop/pmxgentop_log.out:file_utils.py:409 Copying 2564ee00-21fa-4f6e-a008-af4a75176aed/p2g.top to: c1103f63-e595-4858-8aca-c3b2a639c72a\nINFO     /tmp/biobb/unitests_35/pmxgentop/pmxgentop_log.out:file_utils.py:409 Check if c1103f63-e595-4858-8aca-c3b2a639c72a/posre_Protein_chain_A.itp exists\nINFO     /tmp/biobb/unitests_35/pmxgentop/pmxgentop_log.out:file_utils.py:409 Copying 2564ee00-21fa-4f6e-a008-af4a75176aed/posre_Protein_chain_A.itp to: c1103f63-e595-4858-8aca-c3b2a639c72a\nINFO     /tmp/biobb/unitests_35/pmxgentop/pmxgentop_log.out:file_utils.py:409 Check if c1103f63-e595-4858-8aca-c3b2a639c72a/posre_Ion.itp exists\nINFO     /tmp/biobb/unitests_35/pmxgentop/pmxgentop_log.out:file_utils.py:409 Copying 2564ee00-21fa-4f6e-a008-af4a75176aed/posre_Ion.itp to: c1103f63-e595-4858-8aca-c3b2a639c72a\nINFO     /tmp/biobb/unitests_35/pmxgentop/pmxgentop_log.out:file_utils.py:409 Compressing topology to: /tmp/biobb/unitests_35/pmxgentop/output_topology.zip\nINFO     /tmp/biobb/unitests_35/pmxgentop/pmxgentop_log.out:file_utils.py:203 Ignored file c1103f63-e595-4858-8aca-c3b2a639c72a/amber99sb-star-ildn-mut.ff/forcefield.itp\nINFO     /tmp/biobb/unitests_35/pmxgentop/pmxgentop_log.out:file_utils.py:203 Ignored file c1103f63-e595-4858-8aca-c3b2a639c72a/amber99sb-star-ildn-mut.ff/spce.itp\nINFO     /tmp/biobb/unitests_35/pmxgentop/pmxgentop_log.out:file_utils.py:203 Ignored file c1103f63-e595-4858-8aca-c3b2a639c72a/amber99sb-star-ildn-mut.ff/ions.itp\nINFO     /tmp/biobb/unitests_35/pmxgentop/pmxgentop_log.out:file_utils.py:148 Adding:\nINFO     /tmp/biobb/unitests_35/pmxgentop/pmxgentop_log.out:file_utils.py:149 [&amp;#x27;c1103f63-e595-4858-8aca-c3b2a639c72a/pmx_p2g_Ion.itp&amp;#x27;, &amp;#x27;c1103f63-e595-4858-8aca-c3b2a639c72a/pmx_p2g_Protein_chain_A.itp&amp;#x27;, &amp;#x27;c1103f63-e595-4858-8aca-c3b2a639c72a/pmxgentop_p2g.top&amp;#x27;, &amp;#x27;c1103f63-e595-4858-8aca-c3b2a639c72a/posre_Ion.itp&amp;#x27;, &amp;#x27;c1103f63-e595-4858-8aca-c3b2a639c72a/posre_Protein_chain_A.itp&amp;#x27;]\nINFO     /tmp/biobb/unitests_35/pmxgentop/pmxgentop_log.out:file_utils.py:150 to: /tmp/biobb/unitests_35/pmxgentop/output_topology.zip\nINFO     /tmp/biobb/unitests_35/pmxgentop/pmxgentop_log.out:file_utils.py:409 Removed: [&amp;#x27;c1103f63-e595-4858-8aca-c3b2a639c72a/posre_Protein_chain_A.itp&amp;#x27;, &amp;#x27;c1103f63-e595-4858-8aca-c3b2a639c72a/pmx_p2g_Protein_chain_A.itp&amp;#x27;, &amp;#x27;c1103f63-e595-4858-8aca-c3b2a639c72a/posre_Ion.itp&amp;#x27;, &amp;#x27;c1103f63-e595-4858-8aca-c3b2a639c72a/pmx_p2g_Ion.itp&amp;#x27;, &amp;#x27;c1103f63-e595-4858-8aca-c3b2a639c72a/pmxgentop_p2g.top&amp;#x27;]\nINFO     /tmp/biobb/unitests_35/pmxgentop/pmxgentop_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_35\n&#34;}], &#34;biobb_pmx/test/unitests/test_pmx/test_pmxligand_hybrid.py::TestPmxligand_hybrid::test_pmxligand_hybrid&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_pmx/test/unitests/test_pmx/test_pmxligand_hybrid.py::TestPmxligand_hybrid::test_pmxligand_hybrid&#34;, &#34;duration&#34;: &#34;00:00:02&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_pmx/test/unitests/test_pmx/test_pmxligand_hybrid.py::TestPmxligand_hybrid::test_pmxligand_hybrid&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:00:02&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-11-04 15:33:22,351 [MainThread  ] [INFO ]  Module: biobb_pmx.pmxbiobb.pmxligand_hybrid Version: 4.2.1\n2024-11-04 15:33:22,351 [MainThread  ] [INFO ]  /tmp/biobb/unitests_35/pmxligand_hybrid/sandbox_2ca8b37e-3258-45ca-a616-ce98d789aa1c directory successfully created\n2024-11-04 15:33:22,351 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/lig1.pdb to /tmp/biobb/unitests_35/pmxligand_hybrid/sandbox_2ca8b37e-3258-45ca-a616-ce98d789aa1c\n2024-11-04 15:33:22,352 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/lig2.pdb to /tmp/biobb/unitests_35/pmxligand_hybrid/sandbox_2ca8b37e-3258-45ca-a616-ce98d789aa1c\n2024-11-04 15:33:22,352 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/topoLig1.itp to /tmp/biobb/unitests_35/pmxligand_hybrid/sandbox_2ca8b37e-3258-45ca-a616-ce98d789aa1c\n2024-11-04 15:33:22,352 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/topoLig2.itp to /tmp/biobb/unitests_35/pmxligand_hybrid/sandbox_2ca8b37e-3258-45ca-a616-ce98d789aa1c\n2024-11-04 15:33:22,352 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/myPairs1.dat to /tmp/biobb/unitests_35/pmxligand_hybrid/sandbox_2ca8b37e-3258-45ca-a616-ce98d789aa1c\n2024-11-04 15:33:22,353 [MainThread  ] [INFO ]  pmx ligandHybrid -i1 /tmp/biobb/unitests_35/pmxligand_hybrid/sandbox_2ca8b37e-3258-45ca-a616-ce98d789aa1c/lig1.pdb -i2 /tmp/biobb/unitests_35/pmxligand_hybrid/sandbox_2ca8b37e-3258-45ca-a616-ce98d789aa1c/lig2.pdb -itp1 /tmp/biobb/unitests_35/pmxligand_hybrid/sandbox_2ca8b37e-3258-45ca-a616-ce98d789aa1c/topoLig1.itp -itp2 /tmp/biobb/unitests_35/pmxligand_hybrid/sandbox_2ca8b37e-3258-45ca-a616-ce98d789aa1c/topoLig2.itp -pairs /tmp/biobb/unitests_35/pmxligand_hybrid/sandbox_2ca8b37e-3258-45ca-a616-ce98d789aa1c/myPairs1.dat -oA /tmp/biobb/unitests_35/pmxligand_hybrid/sandbox_2ca8b37e-3258-45ca-a616-ce98d789aa1c/hybridStruct1.pdb -oB /tmp/biobb/unitests_35/pmxligand_hybrid/sandbox_2ca8b37e-3258-45ca-a616-ce98d789aa1c/hybridStruct2.pdb -oitp /tmp/biobb/unitests_35/pmxligand_hybrid/sandbox_2ca8b37e-3258-45ca-a616-ce98d789aa1c/hybridTopo.itp -offitp /tmp/biobb/unitests_35/pmxligand_hybrid/sandbox_2ca8b37e-3258-45ca-a616-ce98d789aa1c/hybridAtomTypes.itp -log /tmp/biobb/unitests_35/pmxligand_hybrid/sandbox_2ca8b37e-3258-45ca-a616-ce98d789aa1c/ligand_hybrid.log --fit --d 0.05\n\n2024-11-04 15:33:24,124 [MainThread  ] [INFO ]  Executing: pmx ligandHybrid -i1 /tmp/biobb/unitests_35/pmxligand_hybrid/sandbox_2ca8b37e-32...\n2024-11-04 15:33:24,124 [MainThread  ] [INFO ]  Exit code: 0\n2024-11-04 15:33:24,124 [MainThread  ] [INFO ]  ligandHybridTop__log_&amp;gt; Reading ligand 1 from: &amp;quot;/tmp/biobb/unitests_35/pmxligand_hybrid/sandbox_2ca8b37e-3258-45ca-a616-ce98d789aa1c/lig1.pdb&amp;quot;\nligandHybridTop__log_&amp;gt; Reading ligand 2 from: &amp;quot;/tmp/biobb/unitests_35/pmxligand_hybrid/sandbox_2ca8b37e-3258-45ca-a616-ce98d789aa1c/lig2.pdb&amp;quot;\nligandHybridTop__log_&amp;gt; Reading topology 1 from: &amp;quot;/tmp/biobb/unitests_35/pmxligand_hybrid/sandbox_2ca8b37e-3258-45ca-a616-ce98d789aa1c/topoLig1.itp&amp;quot;\nligandHybridTop__log_&amp;gt; Reading topology 2 from: &amp;quot;/tmp/biobb/unitests_35/pmxligand_hybrid/sandbox_2ca8b37e-3258-45ca-a616-ce98d789aa1c/topoLig2.itp&amp;quot;\nligandHybridTop__log_&amp;gt; Reading file with atom pairs: &amp;quot;/tmp/biobb/unitests_35/pmxligand_hybrid/sandbox_2ca8b37e-3258-45ca-a616-ce98d789aa1c/myPairs1.dat&amp;quot;\nligandHybridTop__log_&amp;gt; Assigning forcefield parameters....\nligandHybridTop__log_&amp;gt; Superimposing mol2 on mol1\nligandHybridTop__log_&amp;gt; Superimposing mol1 on mol2\nligandHybridTop__log_&amp;gt; Initializing the main object for LigandHybridTopology\nligandHybridTop__log_&amp;gt; Starting hybrid topology generation\nligandHybridTop__log_&amp;gt; Making atom pairs.....\nligandHybridTop__log_&amp;gt; Identifying dummies.....\nligandHybridTop__log_&amp;gt; Generated 33 atom-atom pairs\nligandHybridTop__log_&amp;gt; Dummies in state A: 6\nligandHybridTop__log_&amp;gt; Dummies in state B: 6\nligandHybridTop__log_&amp;gt; Making B-states....\nligandHybridTop__log_&amp;gt; Atom....:    2            c3 |   0.14 |  12.01 -&amp;gt;           c3 |   0.14 |  12.01\nligandHybridTop__log_&amp;gt; Atom....:   27            h1 |   0.05 |   1.01 -&amp;gt;           h1 |   0.05 |   1.01\nligandHybridTop__log_&amp;gt; Atom....:   28            h1 |   0.05 |   1.01 -&amp;gt;           h1 |   0.05 |   1.01\nligandHybridTop__log_&amp;gt; Atom....:    1            c3 |  -0.11 |  12.01 -&amp;gt;           c3 |  -0.11 |  12.01\nligandHybridTop__log_&amp;gt; Atom....:   24            hc |   0.05 |   1.01 -&amp;gt;           hc |   0.05 |   1.01\nligandHybridTop__log_&amp;gt; Atom....:   25            hc |   0.05 |   1.01 -&amp;gt;           hc |   0.05 |   1.01\nligandHybridTop__log_&amp;gt; Atom....:   26            hc |   0.05 |   1.01 -&amp;gt;           hc |   0.05 |   1.01\nligandHybridTop__log_&amp;gt; Atom....:    3            os |  -0.44 |  16.00 -&amp;gt;           os |  -0.44 |  16.00\nligandHybridTop__log_&amp;gt; Atom....:    4            ca |   0.74 |  12.01 -&amp;gt;           ca |   0.74 |  12.01\nligandHybridTop__log_&amp;gt; Atom....:    5            nb |  -0.83 |  14.01 -&amp;gt;           nb |  -0.83 |  14.01\nligandHybridTop__log_&amp;gt; Atom....:    6            ca |   0.63 |  12.01 -&amp;gt;           ca |   0.62 |  12.01\nligandHybridTop__log_&amp;gt; Atom....:    7            ca |  -0.39 |  12.01 -&amp;gt;           ca |  -0.39 |  12.01\nligandHybridTop__log_&amp;gt; Atom....:   29            ha |   0.18 |   1.01 -&amp;gt;           ha |   0.18 |   1.01\nligandHybridTop__log_&amp;gt; Atom....:    8            ca |   0.31 |  12.01 -&amp;gt;           ca |   0.31 |  12.01\nligandHybridTop__log_&amp;gt; Atom....:   10            ca |  -0.28 |  12.01 -&amp;gt;           ca |  -0.28 |  12.01\nligandHybridTop__log_&amp;gt; Atom....:   11            cg |   0.27 |  12.01 -&amp;gt;           cg |   0.27 |  12.01\nligandHybridTop__log_&amp;gt; Atom....:   12            n1 |  -0.39 |  14.01 -&amp;gt;           n1 |  -0.39 |  14.01\nligandHybridTop__log_&amp;gt; Atom....:    9            nv |  -0.86 |  14.01 -&amp;gt;           nv |  -0.86 |  14.01\nligandHybridTop__log_&amp;gt; Atom....:   13            ns |  -0.55 |  14.01 -&amp;gt;           ns |  -0.55 |  14.01\nligandHybridTop__log_&amp;gt; Atom....:   14             c |   0.68 |  12.01 -&amp;gt;            c |   0.67 |  12.01\nligandHybridTop__log_&amp;gt; Atom....:   15             o |  -0.58 |  16.00 -&amp;gt;            o |  -0.58 |  16.00\nligandHybridTop__log_&amp;gt; Atom....:   16            c3 |  -0.11 |  12.01 -&amp;gt;           c3 |  -0.11 |  12.01\nligandHybridTop__log_&amp;gt; Atom....:   33            hc |   0.09 |   1.01 -&amp;gt;           hc |   0.09 |   1.01\nligandHybridTop__log_&amp;gt; Atom....:   34            hc |   0.09 |   1.01 -&amp;gt;           hc |   0.09 |   1.01\nligandHybridTop__log_&amp;gt; Atom....:   17            ca |  -0.10 |  12.01 -&amp;gt;           ca |  -0.09 |  12.01\nligandHybridTop__log_&amp;gt; Atom....:   18            ca |   0.03 |  12.01 -&amp;gt;           ca |  -0.11 |  12.01\nligandHybridTop__log_&amp;gt; Atom....:   20            ca |  -0.12 |  12.01 -&amp;gt;           ca |   0.02 |  12.01\nligandHybridTop__log_&amp;gt; Atom....:   21            ca |  -0.11 |  12.01 -&amp;gt;           ca |  -0.12 |  12.01\nligandHybridTop__log_&amp;gt; Atom....:   36            ha |   0.14 |   1.01 -&amp;gt;           ha |   0.15 |   1.01\nligandHybridTop__log_&amp;gt; Atom....:   22            ca |  -0.12 |  12.01 -&amp;gt;           ca |  -0.12 |  12.01\nligandHybridTop__log_&amp;gt; Atom....:   37            ha |   0.14 |   1.01 -&amp;gt;           ha |   0.14 |   1.01\nligandHybridTop__log_&amp;gt; Atom....:   23            ca |  -0.12 |  12.01 -&amp;gt;           ca |  -0.13 |  12.01\nligandHybridTop__log_&amp;gt; Atom....:   38            ha |   0.14 |   1.01 -&amp;gt;           ha |   0.14 |   1.01\nligandHybridTop__log_&amp;gt; Constructing dummies....\nligandHybridTop__log_&amp;gt; Dummies in stateA: \nligandHybridTop__log_&amp;gt; Dummy...:   40        DUM_cl |   0.00 |  35.45 -&amp;gt;           cl |  -0.12 |  35.45\nligandHybridTop__log_&amp;gt; Dummy...:   41        DUM_hn |   0.00 |   1.01 -&amp;gt;           hn |   0.44 |   1.01\nligandHybridTop__log_&amp;gt; Dummy...:   42        DUM_hn |   0.00 |   1.01 -&amp;gt;           hn |   0.44 |   1.01\nligandHybridTop__log_&amp;gt; Dummy...:   43        DUM_hn |   0.00 |   1.01 -&amp;gt;           hn |   0.34 |   1.01\nligandHybridTop__log_&amp;gt; Dummy...:   44        DUM_ha |   0.00 |   1.01 -&amp;gt;           ha |   0.16 |   1.01\nligandHybridTop__log_&amp;gt; Dummy...:   45        DUM_DU |   0.00 |   0.00 -&amp;gt;           DU |   0.04 |   0.00\nligandHybridTop__log_&amp;gt; Dummies in stateB: \nligandHybridTop__log_&amp;gt; Dummy...:   19            cl |  -0.11 |  35.45 -&amp;gt;       DUM_cl |   0.00 |  35.45\nligandHybridTop__log_&amp;gt; Dummy...:   30            hn |   0.44 |   1.01 -&amp;gt;       DUM_hn |   0.00 |   1.01\nligandHybridTop__log_&amp;gt; Dummy...:   31            hn |   0.44 |   1.01 -&amp;gt;       DUM_hn |   0.00 |   1.01\nligandHybridTop__log_&amp;gt; Dummy...:   32            hn |   0.34 |   1.01 -&amp;gt;       DUM_hn |   0.00 |   1.01\nligandHybridTop__log_&amp;gt; Dummy...:   35            ha |   0.15 |   1.01 -&amp;gt;       DUM_ha |   0.00 |   1.01\nligandHybridTop__log_&amp;gt; Dummy...:   39            DU |   0.04 |   0.00 -&amp;gt;       DUM_DU |   0.00 |   0.00\nligandHybridTop__log_&amp;gt; Construct bonds....\nligandHybridTop__log_&amp;gt; Construct angles....\nligandHybridTop__log_&amp;gt; Construct dihedrals....\nligandHybridTop__log_&amp;gt; Construct vsites2....\nligandHybridTop__log_&amp;gt; Construct vsites3....\nligandHybridTop__log_&amp;gt; Construct exclusions....\nligandHybridTop__log_&amp;gt; Construct pairs (1-4 interactions)....\nligandHybridTop__log_&amp;gt; Assembling new itp....\nligandHybridTop__log_&amp;gt; Writing new itp file: &amp;quot;/tmp/biobb/unitests_35/pmxligand_hybrid/sandbox_2ca8b37e-3258-45ca-a616-ce98d789aa1c/hybridTopo.itp&amp;quot;\nligandHybridTop__log_&amp;gt; Writing dummy forcefield file: &amp;quot;/tmp/biobb/unitests_35/pmxligand_hybrid/sandbox_2ca8b37e-3258-45ca-a616-ce98d789aa1c/hybridAtomTypes.itp&amp;quot;\n\n2024-11-04 15:33:24,125 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_35/pmxligand_hybrid/sandbox_2ca8b37e-3258-45ca-a616-ce98d789aa1c&amp;#x27;]\n2024-11-04 15:33:24,126 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_35/pmxligand_hybrid/hybridStruct1.pdb\nChecking if empty file: /tmp/biobb/unitests_35/pmxligand_hybrid/hybridStruct2.pdb\nChecking if empty file: /tmp/biobb/unitests_35/pmxligand_hybrid/hybridTopo.itp\nChecking if empty file: /tmp/biobb/unitests_35/pmxligand_hybrid/hybridAtomTypes.itp\nChecking RMSD between:\n     PDB_A: /tmp/biobb/unitests_35/pmxligand_hybrid/hybridStruct1.pdb\n     PDB_B: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/reference/pmx/ref_hybridStructure1.pdb\n     Ignoring HETAMT in RMSD\n     Ignoring Hydrogen atoms in RMSD\n     Atoms ALIGNED in PDB_A: 26\n     Atoms ALIGNED in PDB_B: 26\n     RMS: 3.850114164176677e-15\n     RMS_CUTOFF: 1\nChecking RMSD between:\n     PDB_A: /tmp/biobb/unitests_35/pmxligand_hybrid/hybridStruct2.pdb\n     PDB_B: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/reference/pmx/ref_hybridStructure2.pdb\n     Ignoring HETAMT in RMSD\n     Ignoring Hydrogen atoms in RMSD\n     Atoms ALIGNED in PDB_A: 26\n     Atoms ALIGNED in PDB_B: 26\n     RMS: 0.1872943529544109\n     RMS_CUTOFF: 1\nComparing TOP/ITP:\n     FILE_A: /tmp/biobb/unitests_35/pmxligand_hybrid/hybridTopo.itp\n     FILE_B: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/reference/pmx/ref_hybridTopology.itp\nComparing TOP/ITP:\n     FILE_A: /tmp/biobb/unitests_35/pmxligand_hybrid/hybridAtomTypes.itp\n     FILE_B: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/reference/pmx/ref_hybridAtomTypes.itp\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_35/pmxligand_hybrid/pmxligand_hybrid_log.out:file_utils.py:409 Module: biobb_pmx.pmxbiobb.pmxligand_hybrid Version: 4.2.1\nINFO     /tmp/biobb/unitests_35/pmxligand_hybrid/pmxligand_hybrid_log.out:file_utils.py:82 /tmp/biobb/unitests_35/pmxligand_hybrid/sandbox_2ca8b37e-3258-45ca-a616-ce98d789aa1c directory successfully created\nINFO     /tmp/biobb/unitests_35/pmxligand_hybrid/pmxligand_hybrid_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/lig1.pdb to /tmp/biobb/unitests_35/pmxligand_hybrid/sandbox_2ca8b37e-3258-45ca-a616-ce98d789aa1c\nINFO     /tmp/biobb/unitests_35/pmxligand_hybrid/pmxligand_hybrid_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/lig2.pdb to /tmp/biobb/unitests_35/pmxligand_hybrid/sandbox_2ca8b37e-3258-45ca-a616-ce98d789aa1c\nINFO     /tmp/biobb/unitests_35/pmxligand_hybrid/pmxligand_hybrid_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/topoLig1.itp to /tmp/biobb/unitests_35/pmxligand_hybrid/sandbox_2ca8b37e-3258-45ca-a616-ce98d789aa1c\nINFO     /tmp/biobb/unitests_35/pmxligand_hybrid/pmxligand_hybrid_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/topoLig2.itp to /tmp/biobb/unitests_35/pmxligand_hybrid/sandbox_2ca8b37e-3258-45ca-a616-ce98d789aa1c\nINFO     /tmp/biobb/unitests_35/pmxligand_hybrid/pmxligand_hybrid_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/myPairs1.dat to /tmp/biobb/unitests_35/pmxligand_hybrid/sandbox_2ca8b37e-3258-45ca-a616-ce98d789aa1c\nINFO     /tmp/biobb/unitests_35/pmxligand_hybrid/pmxligand_hybrid_log.out:cmd_wrapper.py:63 pmx ligandHybrid -i1 /tmp/biobb/unitests_35/pmxligand_hybrid/sandbox_2ca8b37e-3258-45ca-a616-ce98d789aa1c/lig1.pdb -i2 /tmp/biobb/unitests_35/pmxligand_hybrid/sandbox_2ca8b37e-3258-45ca-a616-ce98d789aa1c/lig2.pdb -itp1 /tmp/biobb/unitests_35/pmxligand_hybrid/sandbox_2ca8b37e-3258-45ca-a616-ce98d789aa1c/topoLig1.itp -itp2 /tmp/biobb/unitests_35/pmxligand_hybrid/sandbox_2ca8b37e-3258-45ca-a616-ce98d789aa1c/topoLig2.itp -pairs /tmp/biobb/unitests_35/pmxligand_hybrid/sandbox_2ca8b37e-3258-45ca-a616-ce98d789aa1c/myPairs1.dat -oA /tmp/biobb/unitests_35/pmxligand_hybrid/sandbox_2ca8b37e-3258-45ca-a616-ce98d789aa1c/hybridStruct1.pdb -oB /tmp/biobb/unitests_35/pmxligand_hybrid/sandbox_2ca8b37e-3258-45ca-a616-ce98d789aa1c/hybridStruct2.pdb -oitp /tmp/biobb/unitests_35/pmxligand_hybrid/sandbox_2ca8b37e-3258-45ca-a616-ce98d789aa1c/hybridTopo.itp -offitp /tmp/biobb/unitests_35/pmxligand_hybrid/sandbox_2ca8b37e-3258-45ca-a616-ce98d789aa1c/hybridAtomTypes.itp -log /tmp/biobb/unitests_35/pmxligand_hybrid/sandbox_2ca8b37e-3258-45ca-a616-ce98d789aa1c/ligand_hybrid.log --fit --d 0.05\n\nINFO     /tmp/biobb/unitests_35/pmxligand_hybrid/pmxligand_hybrid_log.out:cmd_wrapper.py:36 Executing: pmx ligandHybrid -i1 /tmp/biobb/unitests_35/pmxligand_hybrid/sandbox_2ca8b37e-32...\nINFO     /tmp/biobb/unitests_35/pmxligand_hybrid/pmxligand_hybrid_log.out:cmd_wrapper.py:37 Exit code: 0\nINFO     /tmp/biobb/unitests_35/pmxligand_hybrid/pmxligand_hybrid_log.out:cmd_wrapper.py:41 ligandHybridTop__log_&amp;gt; Reading ligand 1 from: &amp;quot;/tmp/biobb/unitests_35/pmxligand_hybrid/sandbox_2ca8b37e-3258-45ca-a616-ce98d789aa1c/lig1.pdb&amp;quot;\nligandHybridTop__log_&amp;gt; Reading ligand 2 from: &amp;quot;/tmp/biobb/unitests_35/pmxligand_hybrid/sandbox_2ca8b37e-3258-45ca-a616-ce98d789aa1c/lig2.pdb&amp;quot;\nligandHybridTop__log_&amp;gt; Reading topology 1 from: &amp;quot;/tmp/biobb/unitests_35/pmxligand_hybrid/sandbox_2ca8b37e-3258-45ca-a616-ce98d789aa1c/topoLig1.itp&amp;quot;\nligandHybridTop__log_&amp;gt; Reading topology 2 from: &amp;quot;/tmp/biobb/unitests_35/pmxligand_hybrid/sandbox_2ca8b37e-3258-45ca-a616-ce98d789aa1c/topoLig2.itp&amp;quot;\nligandHybridTop__log_&amp;gt; Reading file with atom pairs: &amp;quot;/tmp/biobb/unitests_35/pmxligand_hybrid/sandbox_2ca8b37e-3258-45ca-a616-ce98d789aa1c/myPairs1.dat&amp;quot;\nligandHybridTop__log_&amp;gt; Assigning forcefield parameters....\nligandHybridTop__log_&amp;gt; Superimposing mol2 on mol1\nligandHybridTop__log_&amp;gt; Superimposing mol1 on mol2\nligandHybridTop__log_&amp;gt; Initializing the main object for LigandHybridTopology\nligandHybridTop__log_&amp;gt; Starting hybrid topology generation\nligandHybridTop__log_&amp;gt; Making atom pairs.....\nligandHybridTop__log_&amp;gt; Identifying dummies.....\nligandHybridTop__log_&amp;gt; Generated 33 atom-atom pairs\nligandHybridTop__log_&amp;gt; Dummies in state A: 6\nligandHybridTop__log_&amp;gt; Dummies in state B: 6\nligandHybridTop__log_&amp;gt; Making B-states....\nligandHybridTop__log_&amp;gt; Atom....:    2            c3 |   0.14 |  12.01 -&amp;gt;           c3 |   0.14 |  12.01\nligandHybridTop__log_&amp;gt; Atom....:   27            h1 |   0.05 |   1.01 -&amp;gt;           h1 |   0.05 |   1.01\nligandHybridTop__log_&amp;gt; Atom....:   28            h1 |   0.05 |   1.01 -&amp;gt;           h1 |   0.05 |   1.01\nligandHybridTop__log_&amp;gt; Atom....:    1            c3 |  -0.11 |  12.01 -&amp;gt;           c3 |  -0.11 |  12.01\nligandHybridTop__log_&amp;gt; Atom....:   24            hc |   0.05 |   1.01 -&amp;gt;           hc |   0.05 |   1.01\nligandHybridTop__log_&amp;gt; Atom....:   25            hc |   0.05 |   1.01 -&amp;gt;           hc |   0.05 |   1.01\nligandHybridTop__log_&amp;gt; Atom....:   26            hc |   0.05 |   1.01 -&amp;gt;           hc |   0.05 |   1.01\nligandHybridTop__log_&amp;gt; Atom....:    3            os |  -0.44 |  16.00 -&amp;gt;           os |  -0.44 |  16.00\nligandHybridTop__log_&amp;gt; Atom....:    4            ca |   0.74 |  12.01 -&amp;gt;           ca |   0.74 |  12.01\nligandHybridTop__log_&amp;gt; Atom....:    5            nb |  -0.83 |  14.01 -&amp;gt;           nb |  -0.83 |  14.01\nligandHybridTop__log_&amp;gt; Atom....:    6            ca |   0.63 |  12.01 -&amp;gt;           ca |   0.62 |  12.01\nligandHybridTop__log_&amp;gt; Atom....:    7            ca |  -0.39 |  12.01 -&amp;gt;           ca |  -0.39 |  12.01\nligandHybridTop__log_&amp;gt; Atom....:   29            ha |   0.18 |   1.01 -&amp;gt;           ha |   0.18 |   1.01\nligandHybridTop__log_&amp;gt; Atom....:    8            ca |   0.31 |  12.01 -&amp;gt;           ca |   0.31 |  12.01\nligandHybridTop__log_&amp;gt; Atom....:   10            ca |  -0.28 |  12.01 -&amp;gt;           ca |  -0.28 |  12.01\nligandHybridTop__log_&amp;gt; Atom....:   11            cg |   0.27 |  12.01 -&amp;gt;           cg |   0.27 |  12.01\nligandHybridTop__log_&amp;gt; Atom....:   12            n1 |  -0.39 |  14.01 -&amp;gt;           n1 |  -0.39 |  14.01\nligandHybridTop__log_&amp;gt; Atom....:    9            nv |  -0.86 |  14.01 -&amp;gt;           nv |  -0.86 |  14.01\nligandHybridTop__log_&amp;gt; Atom....:   13            ns |  -0.55 |  14.01 -&amp;gt;           ns |  -0.55 |  14.01\nligandHybridTop__log_&amp;gt; Atom....:   14             c |   0.68 |  12.01 -&amp;gt;            c |   0.67 |  12.01\nligandHybridTop__log_&amp;gt; Atom....:   15             o |  -0.58 |  16.00 -&amp;gt;            o |  -0.58 |  16.00\nligandHybridTop__log_&amp;gt; Atom....:   16            c3 |  -0.11 |  12.01 -&amp;gt;           c3 |  -0.11 |  12.01\nligandHybridTop__log_&amp;gt; Atom....:   33            hc |   0.09 |   1.01 -&amp;gt;           hc |   0.09 |   1.01\nligandHybridTop__log_&amp;gt; Atom....:   34            hc |   0.09 |   1.01 -&amp;gt;           hc |   0.09 |   1.01\nligandHybridTop__log_&amp;gt; Atom....:   17            ca |  -0.10 |  12.01 -&amp;gt;           ca |  -0.09 |  12.01\nligandHybridTop__log_&amp;gt; Atom....:   18            ca |   0.03 |  12.01 -&amp;gt;           ca |  -0.11 |  12.01\nligandHybridTop__log_&amp;gt; Atom....:   20            ca |  -0.12 |  12.01 -&amp;gt;           ca |   0.02 |  12.01\nligandHybridTop__log_&amp;gt; Atom....:   21            ca |  -0.11 |  12.01 -&amp;gt;           ca |  -0.12 |  12.01\nligandHybridTop__log_&amp;gt; Atom....:   36            ha |   0.14 |   1.01 -&amp;gt;           ha |   0.15 |   1.01\nligandHybridTop__log_&amp;gt; Atom....:   22            ca |  -0.12 |  12.01 -&amp;gt;           ca |  -0.12 |  12.01\nligandHybridTop__log_&amp;gt; Atom....:   37            ha |   0.14 |   1.01 -&amp;gt;           ha |   0.14 |   1.01\nligandHybridTop__log_&amp;gt; Atom....:   23            ca |  -0.12 |  12.01 -&amp;gt;           ca |  -0.13 |  12.01\nligandHybridTop__log_&amp;gt; Atom....:   38            ha |   0.14 |   1.01 -&amp;gt;           ha |   0.14 |   1.01\nligandHybridTop__log_&amp;gt; Constructing dummies....\nligandHybridTop__log_&amp;gt; Dummies in stateA: \nligandHybridTop__log_&amp;gt; Dummy...:   40        DUM_cl |   0.00 |  35.45 -&amp;gt;           cl |  -0.12 |  35.45\nligandHybridTop__log_&amp;gt; Dummy...:   41        DUM_hn |   0.00 |   1.01 -&amp;gt;           hn |   0.44 |   1.01\nligandHybridTop__log_&amp;gt; Dummy...:   42        DUM_hn |   0.00 |   1.01 -&amp;gt;           hn |   0.44 |   1.01\nligandHybridTop__log_&amp;gt; Dummy...:   43        DUM_hn |   0.00 |   1.01 -&amp;gt;           hn |   0.34 |   1.01\nligandHybridTop__log_&amp;gt; Dummy...:   44        DUM_ha |   0.00 |   1.01 -&amp;gt;           ha |   0.16 |   1.01\nligandHybridTop__log_&amp;gt; Dummy...:   45        DUM_DU |   0.00 |   0.00 -&amp;gt;           DU |   0.04 |   0.00\nligandHybridTop__log_&amp;gt; Dummies in stateB: \nligandHybridTop__log_&amp;gt; Dummy...:   19            cl |  -0.11 |  35.45 -&amp;gt;       DUM_cl |   0.00 |  35.45\nligandHybridTop__log_&amp;gt; Dummy...:   30            hn |   0.44 |   1.01 -&amp;gt;       DUM_hn |   0.00 |   1.01\nligandHybridTop__log_&amp;gt; Dummy...:   31            hn |   0.44 |   1.01 -&amp;gt;       DUM_hn |   0.00 |   1.01\nligandHybridTop__log_&amp;gt; Dummy...:   32            hn |   0.34 |   1.01 -&amp;gt;       DUM_hn |   0.00 |   1.01\nligandHybridTop__log_&amp;gt; Dummy...:   35            ha |   0.15 |   1.01 -&amp;gt;       DUM_ha |   0.00 |   1.01\nligandHybridTop__log_&amp;gt; Dummy...:   39            DU |   0.04 |   0.00 -&amp;gt;       DUM_DU |   0.00 |   0.00\nligandHybridTop__log_&amp;gt; Construct bonds....\nligandHybridTop__log_&amp;gt; Construct angles....\nligandHybridTop__log_&amp;gt; Construct dihedrals....\nligandHybridTop__log_&amp;gt; Construct vsites2....\nligandHybridTop__log_&amp;gt; Construct vsites3....\nligandHybridTop__log_&amp;gt; Construct exclusions....\nligandHybridTop__log_&amp;gt; Construct pairs (1-4 interactions)....\nligandHybridTop__log_&amp;gt; Assembling new itp....\nligandHybridTop__log_&amp;gt; Writing new itp file: &amp;quot;/tmp/biobb/unitests_35/pmxligand_hybrid/sandbox_2ca8b37e-3258-45ca-a616-ce98d789aa1c/hybridTopo.itp&amp;quot;\nligandHybridTop__log_&amp;gt; Writing dummy forcefield file: &amp;quot;/tmp/biobb/unitests_35/pmxligand_hybrid/sandbox_2ca8b37e-3258-45ca-a616-ce98d789aa1c/hybridAtomTypes.itp&amp;quot;\n\nINFO     /tmp/biobb/unitests_35/pmxligand_hybrid/pmxligand_hybrid_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_35/pmxligand_hybrid/sandbox_2ca8b37e-3258-45ca-a616-ce98d789aa1c&amp;#x27;]\nINFO     /tmp/biobb/unitests_35/pmxligand_hybrid/pmxligand_hybrid_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_35\n&#34;}], &#34;biobb_pmx/test/unitests/test_pmx/test_pmxmerge_ff.py::TestPmxmerge_ff::test_pmxmerge_ff&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_pmx/test/unitests/test_pmx/test_pmxmerge_ff.py::TestPmxmerge_ff::test_pmxmerge_ff&#34;, &#34;duration&#34;: &#34;32 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_pmx/test/unitests/test_pmx/test_pmxmerge_ff.py::TestPmxmerge_ff::test_pmxmerge_ff&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;32 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-11-04 15:33:24,169 [MainThread  ] [INFO ]  Module: biobb_pmx.pmxbiobb.pmxmerge_ff Version: 4.2.1\n2024-11-04 15:33:24,169 [MainThread  ] [INFO ]  /tmp/biobb/unitests_35/pmxmerge_ff/sandbox_8bd02e35-42a9-4e80-a2a3-516d56834c23 directory successfully created\n2024-11-04 15:33:24,169 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/itps_to_merge.zip to /tmp/biobb/unitests_35/pmxmerge_ff/sandbox_8bd02e35-42a9-4e80-a2a3-516d56834c23\n2024-11-04 15:33:24,170 [MainThread  ] [INFO ]  Creating 46583d50-0901-4f58-b649-82e72ae82360 temporary folder\n2024-11-04 15:33:24,170 [MainThread  ] [INFO ]  Extracting: /tmp/biobb/unitests_35/pmxmerge_ff/sandbox_8bd02e35-42a9-4e80-a2a3-516d56834c23/itps_to_merge.zip\n2024-11-04 15:33:24,170 [MainThread  ] [INFO ]  to:\n2024-11-04 15:33:24,170 [MainThread  ] [INFO ]  [&amp;#x27;46583d50-0901-4f58-b649-82e72ae82360/myHybridAtomTypes.itp&amp;#x27;, &amp;#x27;46583d50-0901-4f58-b649-82e72ae82360/lig1ffMOL.itp&amp;#x27;, &amp;#x27;46583d50-0901-4f58-b649-82e72ae82360/lig2ffMOL.itp&amp;#x27;]\n2024-11-04 15:33:24,171 [MainThread  ] [INFO ]  Running merge_FF_files from pmx package...\n\n2024-11-04 15:33:24,171 [MainThread  ] [INFO ]  Exit code 0\n\n2024-11-04 15:33:24,171 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_35/pmxmerge_ff/sandbox_8bd02e35-42a9-4e80-a2a3-516d56834c23&amp;#x27;]\n2024-11-04 15:33:24,172 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_35/pmxmerge_ff/hybridTopo.itp\nComparing size of both files:\n     FILE_A: /tmp/biobb/unitests_35/pmxmerge_ff/hybridTopo.itp\n     FILE_B: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/reference/pmx/ref_mergedTopology.itp\n     SIZE_A: 1468 bytes\n     SIZE_B: 1468 bytes\n     TOLERANCE: 1.0%, Low: 1453.32 bytes, High: 1482.68 bytes\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_35/pmxmerge_ff/pmxmerge_ff_log.out:file_utils.py:409 Module: biobb_pmx.pmxbiobb.pmxmerge_ff Version: 4.2.1\nINFO     /tmp/biobb/unitests_35/pmxmerge_ff/pmxmerge_ff_log.out:file_utils.py:82 /tmp/biobb/unitests_35/pmxmerge_ff/sandbox_8bd02e35-42a9-4e80-a2a3-516d56834c23 directory successfully created\nINFO     /tmp/biobb/unitests_35/pmxmerge_ff/pmxmerge_ff_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/itps_to_merge.zip to /tmp/biobb/unitests_35/pmxmerge_ff/sandbox_8bd02e35-42a9-4e80-a2a3-516d56834c23\nINFO     /tmp/biobb/unitests_35/pmxmerge_ff/pmxmerge_ff_log.out:file_utils.py:409 Creating 46583d50-0901-4f58-b649-82e72ae82360 temporary folder\nINFO     /tmp/biobb/unitests_35/pmxmerge_ff/pmxmerge_ff_log.out:file_utils.py:172 Extracting: /tmp/biobb/unitests_35/pmxmerge_ff/sandbox_8bd02e35-42a9-4e80-a2a3-516d56834c23/itps_to_merge.zip\nINFO     /tmp/biobb/unitests_35/pmxmerge_ff/pmxmerge_ff_log.out:file_utils.py:173 to:\nINFO     /tmp/biobb/unitests_35/pmxmerge_ff/pmxmerge_ff_log.out:file_utils.py:174 [&amp;#x27;46583d50-0901-4f58-b649-82e72ae82360/myHybridAtomTypes.itp&amp;#x27;, &amp;#x27;46583d50-0901-4f58-b649-82e72ae82360/lig1ffMOL.itp&amp;#x27;, &amp;#x27;46583d50-0901-4f58-b649-82e72ae82360/lig2ffMOL.itp&amp;#x27;]\nINFO     /tmp/biobb/unitests_35/pmxmerge_ff/pmxmerge_ff_log.out:file_utils.py:409 Running merge_FF_files from pmx package...\n\nINFO     /tmp/biobb/unitests_35/pmxmerge_ff/pmxmerge_ff_log.out:file_utils.py:409 Exit code 0\n\nINFO     /tmp/biobb/unitests_35/pmxmerge_ff/pmxmerge_ff_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_35/pmxmerge_ff/sandbox_8bd02e35-42a9-4e80-a2a3-516d56834c23&amp;#x27;]\nINFO     /tmp/biobb/unitests_35/pmxmerge_ff/pmxmerge_ff_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_35\n&#34;}], &#34;biobb_pmx/test/unitests/test_pmx/test_pmxmutate.py::TestPmxmutate::test_pmxmutate&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_pmx/test/unitests/test_pmx/test_pmxmutate.py::TestPmxmutate::test_pmxmutate&#34;, &#34;duration&#34;: &#34;00:00:05&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_pmx/test/unitests/test_pmx/test_pmxmutate.py::TestPmxmutate::test_pmxmutate&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:00:05&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-11-04 15:33:24,202 [MainThread  ] [INFO ]  Module: biobb_pmx.pmxbiobb.pmxmutate Version: 4.2.1\n2024-11-04 15:33:24,202 [MainThread  ] [INFO ]  /tmp/biobb/unitests_35/pmxmutate/sandbox_08068018-51ce-41cb-b31f-30be7ae3b020 directory successfully created\n2024-11-04 15:33:24,204 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/frameA0.pdb to /tmp/biobb/unitests_35/pmxmutate/sandbox_08068018-51ce-41cb-b31f-30be7ae3b020\n2024-11-04 15:33:24,205 [MainThread  ] [INFO ]  pmx mutate -f /tmp/biobb/unitests_35/pmxmutate/sandbox_08068018-51ce-41cb-b31f-30be7ae3b020/frameA0.pdb -o /tmp/biobb/unitests_35/pmxmutate/sandbox_08068018-51ce-41cb-b31f-30be7ae3b020/output_structure.pdb -ff amber99sb-star-ildn-mut --script c28b4088-5c55-4bf6-a91d-d59688e0ccfc/mutations.txt\n\n2024-11-04 15:33:26,964 [MainThread  ] [INFO ]  Executing: pmx mutate -f /tmp/biobb/unitests_35/pmxmutate/sandbox_08068018-51ce-41cb-b31f-3...\n2024-11-04 15:33:26,965 [MainThread  ] [INFO ]  Exit code: 0\n2024-11-04 15:33:26,965 [MainThread  ] [INFO ]  log_&amp;gt; Residue to mutate: 10 | ILE | A \nlog_&amp;gt; Mutation to apply: I-&amp;gt;A\nlog_&amp;gt; Hybrid residue name: I2A\nlog_&amp;gt; Inserted hybrid residue I2A at position 10 (chain A)\n\nmutations done...........\n\n\n2024-11-04 15:33:26,967 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_35/pmxmutate/sandbox_08068018-51ce-41cb-b31f-30be7ae3b020&amp;#x27;]\n2024-11-04 15:33:26,968 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_35/pmxmutate/output_structure.pdb\nChecking RMSD between:\n     PDB_A: /tmp/biobb/unitests_35/pmxmutate/output_structure.pdb\n     PDB_B: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/reference/pmx/ref_output_structure.pdb\n     Ignoring HETAMT in RMSD\n     Ignoring Hydrogen atoms in RMSD\n     Atoms ALIGNED in PDB_A: 11092\n     Atoms ALIGNED in PDB_B: 11092\n     RMS: 2.2084949513674e-14\n     RMS_CUTOFF: 1\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_35/pmxmutate/pmxmutate_log.out:file_utils.py:409 Module: biobb_pmx.pmxbiobb.pmxmutate Version: 4.2.1\nINFO     /tmp/biobb/unitests_35/pmxmutate/pmxmutate_log.out:file_utils.py:82 /tmp/biobb/unitests_35/pmxmutate/sandbox_08068018-51ce-41cb-b31f-30be7ae3b020 directory successfully created\nINFO     /tmp/biobb/unitests_35/pmxmutate/pmxmutate_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/frameA0.pdb to /tmp/biobb/unitests_35/pmxmutate/sandbox_08068018-51ce-41cb-b31f-30be7ae3b020\nINFO     /tmp/biobb/unitests_35/pmxmutate/pmxmutate_log.out:cmd_wrapper.py:63 pmx mutate -f /tmp/biobb/unitests_35/pmxmutate/sandbox_08068018-51ce-41cb-b31f-30be7ae3b020/frameA0.pdb -o /tmp/biobb/unitests_35/pmxmutate/sandbox_08068018-51ce-41cb-b31f-30be7ae3b020/output_structure.pdb -ff amber99sb-star-ildn-mut --script c28b4088-5c55-4bf6-a91d-d59688e0ccfc/mutations.txt\n\nINFO     /tmp/biobb/unitests_35/pmxmutate/pmxmutate_log.out:cmd_wrapper.py:36 Executing: pmx mutate -f /tmp/biobb/unitests_35/pmxmutate/sandbox_08068018-51ce-41cb-b31f-3...\nINFO     /tmp/biobb/unitests_35/pmxmutate/pmxmutate_log.out:cmd_wrapper.py:37 Exit code: 0\nINFO     /tmp/biobb/unitests_35/pmxmutate/pmxmutate_log.out:cmd_wrapper.py:41 log_&amp;gt; Residue to mutate: 10 | ILE | A \nlog_&amp;gt; Mutation to apply: I-&amp;gt;A\nlog_&amp;gt; Hybrid residue name: I2A\nlog_&amp;gt; Inserted hybrid residue I2A at position 10 (chain A)\n\nmutations done...........\n\n\nINFO     /tmp/biobb/unitests_35/pmxmutate/pmxmutate_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_35/pmxmutate/sandbox_08068018-51ce-41cb-b31f-30be7ae3b020&amp;#x27;]\nINFO     /tmp/biobb/unitests_35/pmxmutate/pmxmutate_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: 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