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&amp;#x27;92c0201c-6e07-42ab-a977-d62b22b762d5/frame70/dhdl70.xvg&amp;#x27;, &amp;#x27;92c0201c-6e07-42ab-a977-d62b22b762d5/frame71/dhdl71.xvg&amp;#x27;, &amp;#x27;92c0201c-6e07-42ab-a977-d62b22b762d5/frame72/dhdl72.xvg&amp;#x27;, &amp;#x27;92c0201c-6e07-42ab-a977-d62b22b762d5/frame73/dhdl73.xvg&amp;#x27;, &amp;#x27;92c0201c-6e07-42ab-a977-d62b22b762d5/frame74/dhdl74.xvg&amp;#x27;, &amp;#x27;92c0201c-6e07-42ab-a977-d62b22b762d5/frame75/dhdl75.xvg&amp;#x27;, &amp;#x27;92c0201c-6e07-42ab-a977-d62b22b762d5/frame76/dhdl76.xvg&amp;#x27;, &amp;#x27;92c0201c-6e07-42ab-a977-d62b22b762d5/frame77/dhdl77.xvg&amp;#x27;, &amp;#x27;92c0201c-6e07-42ab-a977-d62b22b762d5/frame78/dhdl78.xvg&amp;#x27;, &amp;#x27;92c0201c-6e07-42ab-a977-d62b22b762d5/frame79/dhdl79.xvg&amp;#x27;, &amp;#x27;92c0201c-6e07-42ab-a977-d62b22b762d5/frame8/dhdl8.xvg&amp;#x27;, &amp;#x27;92c0201c-6e07-42ab-a977-d62b22b762d5/frame80/dhdl80.xvg&amp;#x27;, &amp;#x27;92c0201c-6e07-42ab-a977-d62b22b762d5/frame81/dhdl81.xvg&amp;#x27;, &amp;#x27;92c0201c-6e07-42ab-a977-d62b22b762d5/frame82/dhdl82.xvg&amp;#x27;, &amp;#x27;92c0201c-6e07-42ab-a977-d62b22b762d5/frame83/dhdl83.xvg&amp;#x27;, &amp;#x27;92c0201c-6e07-42ab-a977-d62b22b762d5/frame84/dhdl84.xvg&amp;#x27;, &amp;#x27;92c0201c-6e07-42ab-a977-d62b22b762d5/frame85/dhdl85.xvg&amp;#x27;, &amp;#x27;92c0201c-6e07-42ab-a977-d62b22b762d5/frame86/dhdl86.xvg&amp;#x27;, &amp;#x27;92c0201c-6e07-42ab-a977-d62b22b762d5/frame87/dhdl87.xvg&amp;#x27;, &amp;#x27;92c0201c-6e07-42ab-a977-d62b22b762d5/frame88/dhdl88.xvg&amp;#x27;, &amp;#x27;92c0201c-6e07-42ab-a977-d62b22b762d5/frame89/dhdl89.xvg&amp;#x27;, &amp;#x27;92c0201c-6e07-42ab-a977-d62b22b762d5/frame9/dhdl9.xvg&amp;#x27;, &amp;#x27;92c0201c-6e07-42ab-a977-d62b22b762d5/frame90/dhdl90.xvg&amp;#x27;, &amp;#x27;92c0201c-6e07-42ab-a977-d62b22b762d5/frame91/dhdl91.xvg&amp;#x27;, &amp;#x27;92c0201c-6e07-42ab-a977-d62b22b762d5/frame92/dhdl92.xvg&amp;#x27;, &amp;#x27;92c0201c-6e07-42ab-a977-d62b22b762d5/frame93/dhdl93.xvg&amp;#x27;, &amp;#x27;92c0201c-6e07-42ab-a977-d62b22b762d5/frame94/dhdl94.xvg&amp;#x27;, &amp;#x27;92c0201c-6e07-42ab-a977-d62b22b762d5/frame95/dhdl95.xvg&amp;#x27;, &amp;#x27;92c0201c-6e07-42ab-a977-d62b22b762d5/frame96/dhdl96.xvg&amp;#x27;, &amp;#x27;92c0201c-6e07-42ab-a977-d62b22b762d5/frame97/dhdl97.xvg&amp;#x27;, &amp;#x27;92c0201c-6e07-42ab-a977-d62b22b762d5/frame98/dhdl98.xvg&amp;#x27;, &amp;#x27;92c0201c-6e07-42ab-a977-d62b22b762d5/frame99/dhdl99.xvg&amp;#x27;]\n2024-06-14 18:46:51,896 [MainThread  ] [INFO ]  Extracting: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/xvg_B.zip\n2024-06-14 18:46:51,896 [MainThread  ] [INFO ]  to:\n2024-06-14 18:46:51,896 [MainThread  ] [INFO ]  [&amp;#x27;80a21ac4-5be8-4864-aa0e-91cbea071493/frame0/dhdl0.xvg&amp;#x27;, &amp;#x27;80a21ac4-5be8-4864-aa0e-91cbea071493/frame1/dhdl1.xvg&amp;#x27;, &amp;#x27;80a21ac4-5be8-4864-aa0e-91cbea071493/frame10/dhdl10.xvg&amp;#x27;, 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&amp;#x27;80a21ac4-5be8-4864-aa0e-91cbea071493/frame35/dhdl35.xvg&amp;#x27;, &amp;#x27;80a21ac4-5be8-4864-aa0e-91cbea071493/frame36/dhdl36.xvg&amp;#x27;, &amp;#x27;80a21ac4-5be8-4864-aa0e-91cbea071493/frame37/dhdl37.xvg&amp;#x27;, &amp;#x27;80a21ac4-5be8-4864-aa0e-91cbea071493/frame38/dhdl38.xvg&amp;#x27;, &amp;#x27;80a21ac4-5be8-4864-aa0e-91cbea071493/frame39/dhdl39.xvg&amp;#x27;, &amp;#x27;80a21ac4-5be8-4864-aa0e-91cbea071493/frame4/dhdl4.xvg&amp;#x27;, &amp;#x27;80a21ac4-5be8-4864-aa0e-91cbea071493/frame40/dhdl40.xvg&amp;#x27;, &amp;#x27;80a21ac4-5be8-4864-aa0e-91cbea071493/frame41/dhdl41.xvg&amp;#x27;, &amp;#x27;80a21ac4-5be8-4864-aa0e-91cbea071493/frame42/dhdl42.xvg&amp;#x27;, &amp;#x27;80a21ac4-5be8-4864-aa0e-91cbea071493/frame43/dhdl43.xvg&amp;#x27;, &amp;#x27;80a21ac4-5be8-4864-aa0e-91cbea071493/frame44/dhdl44.xvg&amp;#x27;, &amp;#x27;80a21ac4-5be8-4864-aa0e-91cbea071493/frame45/dhdl45.xvg&amp;#x27;, &amp;#x27;80a21ac4-5be8-4864-aa0e-91cbea071493/frame46/dhdl46.xvg&amp;#x27;, &amp;#x27;80a21ac4-5be8-4864-aa0e-91cbea071493/frame47/dhdl47.xvg&amp;#x27;, &amp;#x27;80a21ac4-5be8-4864-aa0e-91cbea071493/frame48/dhdl48.xvg&amp;#x27;, &amp;#x27;80a21ac4-5be8-4864-aa0e-91cbea071493/frame49/dhdl49.xvg&amp;#x27;, &amp;#x27;80a21ac4-5be8-4864-aa0e-91cbea071493/frame5/dhdl5.xvg&amp;#x27;, &amp;#x27;80a21ac4-5be8-4864-aa0e-91cbea071493/frame50/dhdl50.xvg&amp;#x27;, &amp;#x27;80a21ac4-5be8-4864-aa0e-91cbea071493/frame51/dhdl51.xvg&amp;#x27;, &amp;#x27;80a21ac4-5be8-4864-aa0e-91cbea071493/frame52/dhdl52.xvg&amp;#x27;, &amp;#x27;80a21ac4-5be8-4864-aa0e-91cbea071493/frame53/dhdl53.xvg&amp;#x27;, &amp;#x27;80a21ac4-5be8-4864-aa0e-91cbea071493/frame54/dhdl54.xvg&amp;#x27;, &amp;#x27;80a21ac4-5be8-4864-aa0e-91cbea071493/frame55/dhdl55.xvg&amp;#x27;, &amp;#x27;80a21ac4-5be8-4864-aa0e-91cbea071493/frame56/dhdl56.xvg&amp;#x27;, &amp;#x27;80a21ac4-5be8-4864-aa0e-91cbea071493/frame57/dhdl57.xvg&amp;#x27;, &amp;#x27;80a21ac4-5be8-4864-aa0e-91cbea071493/frame58/dhdl58.xvg&amp;#x27;, &amp;#x27;80a21ac4-5be8-4864-aa0e-91cbea071493/frame59/dhdl59.xvg&amp;#x27;, &amp;#x27;80a21ac4-5be8-4864-aa0e-91cbea071493/frame6/dhdl6.xvg&amp;#x27;, &amp;#x27;80a21ac4-5be8-4864-aa0e-91cbea071493/frame60/dhdl60.xvg&amp;#x27;, &amp;#x27;80a21ac4-5be8-4864-aa0e-91cbea071493/frame61/dhdl61.xvg&amp;#x27;, &amp;#x27;80a21ac4-5be8-4864-aa0e-91cbea071493/frame62/dhdl62.xvg&amp;#x27;, &amp;#x27;80a21ac4-5be8-4864-aa0e-91cbea071493/frame63/dhdl63.xvg&amp;#x27;, &amp;#x27;80a21ac4-5be8-4864-aa0e-91cbea071493/frame64/dhdl64.xvg&amp;#x27;, &amp;#x27;80a21ac4-5be8-4864-aa0e-91cbea071493/frame65/dhdl65.xvg&amp;#x27;, &amp;#x27;80a21ac4-5be8-4864-aa0e-91cbea071493/frame66/dhdl66.xvg&amp;#x27;, &amp;#x27;80a21ac4-5be8-4864-aa0e-91cbea071493/frame67/dhdl67.xvg&amp;#x27;, &amp;#x27;80a21ac4-5be8-4864-aa0e-91cbea071493/frame68/dhdl68.xvg&amp;#x27;, &amp;#x27;80a21ac4-5be8-4864-aa0e-91cbea071493/frame69/dhdl69.xvg&amp;#x27;, &amp;#x27;80a21ac4-5be8-4864-aa0e-91cbea071493/frame7/dhdl7.xvg&amp;#x27;, &amp;#x27;80a21ac4-5be8-4864-aa0e-91cbea071493/frame70/dhdl70.xvg&amp;#x27;, &amp;#x27;80a21ac4-5be8-4864-aa0e-91cbea071493/frame71/dhdl71.xvg&amp;#x27;, &amp;#x27;80a21ac4-5be8-4864-aa0e-91cbea071493/frame72/dhdl72.xvg&amp;#x27;, &amp;#x27;80a21ac4-5be8-4864-aa0e-91cbea071493/frame73/dhdl73.xvg&amp;#x27;, &amp;#x27;80a21ac4-5be8-4864-aa0e-91cbea071493/frame74/dhdl74.xvg&amp;#x27;, &amp;#x27;80a21ac4-5be8-4864-aa0e-91cbea071493/frame75/dhdl75.xvg&amp;#x27;, &amp;#x27;80a21ac4-5be8-4864-aa0e-91cbea071493/frame76/dhdl76.xvg&amp;#x27;, &amp;#x27;80a21ac4-5be8-4864-aa0e-91cbea071493/frame77/dhdl77.xvg&amp;#x27;, &amp;#x27;80a21ac4-5be8-4864-aa0e-91cbea071493/frame78/dhdl78.xvg&amp;#x27;, &amp;#x27;80a21ac4-5be8-4864-aa0e-91cbea071493/frame79/dhdl79.xvg&amp;#x27;, &amp;#x27;80a21ac4-5be8-4864-aa0e-91cbea071493/frame8/dhdl8.xvg&amp;#x27;, &amp;#x27;80a21ac4-5be8-4864-aa0e-91cbea071493/frame80/dhdl80.xvg&amp;#x27;, &amp;#x27;80a21ac4-5be8-4864-aa0e-91cbea071493/frame81/dhdl81.xvg&amp;#x27;, &amp;#x27;80a21ac4-5be8-4864-aa0e-91cbea071493/frame82/dhdl82.xvg&amp;#x27;, &amp;#x27;80a21ac4-5be8-4864-aa0e-91cbea071493/frame83/dhdl83.xvg&amp;#x27;, &amp;#x27;80a21ac4-5be8-4864-aa0e-91cbea071493/frame84/dhdl84.xvg&amp;#x27;, &amp;#x27;80a21ac4-5be8-4864-aa0e-91cbea071493/frame85/dhdl85.xvg&amp;#x27;, &amp;#x27;80a21ac4-5be8-4864-aa0e-91cbea071493/frame86/dhdl86.xvg&amp;#x27;, &amp;#x27;80a21ac4-5be8-4864-aa0e-91cbea071493/frame87/dhdl87.xvg&amp;#x27;, &amp;#x27;80a21ac4-5be8-4864-aa0e-91cbea071493/frame88/dhdl88.xvg&amp;#x27;, &amp;#x27;80a21ac4-5be8-4864-aa0e-91cbea071493/frame89/dhdl89.xvg&amp;#x27;, &amp;#x27;80a21ac4-5be8-4864-aa0e-91cbea071493/frame9/dhdl9.xvg&amp;#x27;, &amp;#x27;80a21ac4-5be8-4864-aa0e-91cbea071493/frame90/dhdl90.xvg&amp;#x27;, &amp;#x27;80a21ac4-5be8-4864-aa0e-91cbea071493/frame91/dhdl91.xvg&amp;#x27;, &amp;#x27;80a21ac4-5be8-4864-aa0e-91cbea071493/frame92/dhdl92.xvg&amp;#x27;, &amp;#x27;80a21ac4-5be8-4864-aa0e-91cbea071493/frame93/dhdl93.xvg&amp;#x27;, &amp;#x27;80a21ac4-5be8-4864-aa0e-91cbea071493/frame94/dhdl94.xvg&amp;#x27;, &amp;#x27;80a21ac4-5be8-4864-aa0e-91cbea071493/frame95/dhdl95.xvg&amp;#x27;, &amp;#x27;80a21ac4-5be8-4864-aa0e-91cbea071493/frame96/dhdl96.xvg&amp;#x27;, &amp;#x27;80a21ac4-5be8-4864-aa0e-91cbea071493/frame97/dhdl97.xvg&amp;#x27;, &amp;#x27;80a21ac4-5be8-4864-aa0e-91cbea071493/frame98/dhdl98.xvg&amp;#x27;, &amp;#x27;80a21ac4-5be8-4864-aa0e-91cbea071493/frame99/dhdl99.xvg&amp;#x27;]\n2024-06-14 18:46:51,899 [MainThread  ] [INFO ]  pmx analyse -fA 92c0201c-6e07-42ab-a977-d62b22b762d5/frame0/dhdl0.xvg 92c0201c-6e07-42ab-a977-d62b22b762d5/frame1/dhdl1.xvg 92c0201c-6e07-42ab-a977-d62b22b762d5/frame10/dhdl10.xvg 92c0201c-6e07-42ab-a977-d62b22b762d5/frame11/dhdl11.xvg 92c0201c-6e07-42ab-a977-d62b22b762d5/frame12/dhdl12.xvg 92c0201c-6e07-42ab-a977-d62b22b762d5/frame13/dhdl13.xvg 92c0201c-6e07-42ab-a977-d62b22b762d5/frame14/dhdl14.xvg 92c0201c-6e07-42ab-a977-d62b22b762d5/frame15/dhdl15.xvg 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80a21ac4-5be8-4864-aa0e-91cbea071493/frame8/dhdl8.xvg 80a21ac4-5be8-4864-aa0e-91cbea071493/frame80/dhdl80.xvg 80a21ac4-5be8-4864-aa0e-91cbea071493/frame81/dhdl81.xvg 80a21ac4-5be8-4864-aa0e-91cbea071493/frame82/dhdl82.xvg 80a21ac4-5be8-4864-aa0e-91cbea071493/frame83/dhdl83.xvg 80a21ac4-5be8-4864-aa0e-91cbea071493/frame84/dhdl84.xvg 80a21ac4-5be8-4864-aa0e-91cbea071493/frame85/dhdl85.xvg 80a21ac4-5be8-4864-aa0e-91cbea071493/frame86/dhdl86.xvg 80a21ac4-5be8-4864-aa0e-91cbea071493/frame87/dhdl87.xvg 80a21ac4-5be8-4864-aa0e-91cbea071493/frame88/dhdl88.xvg 80a21ac4-5be8-4864-aa0e-91cbea071493/frame89/dhdl89.xvg 80a21ac4-5be8-4864-aa0e-91cbea071493/frame9/dhdl9.xvg 80a21ac4-5be8-4864-aa0e-91cbea071493/frame90/dhdl90.xvg 80a21ac4-5be8-4864-aa0e-91cbea071493/frame91/dhdl91.xvg 80a21ac4-5be8-4864-aa0e-91cbea071493/frame92/dhdl92.xvg 80a21ac4-5be8-4864-aa0e-91cbea071493/frame93/dhdl93.xvg 80a21ac4-5be8-4864-aa0e-91cbea071493/frame94/dhdl94.xvg 80a21ac4-5be8-4864-aa0e-91cbea071493/frame95/dhdl95.xvg 80a21ac4-5be8-4864-aa0e-91cbea071493/frame96/dhdl96.xvg 80a21ac4-5be8-4864-aa0e-91cbea071493/frame97/dhdl97.xvg 80a21ac4-5be8-4864-aa0e-91cbea071493/frame98/dhdl98.xvg 80a21ac4-5be8-4864-aa0e-91cbea071493/frame99/dhdl99.xvg -o /tmp/biobb/unitests_167/pmxanalyse/sandbox_255a2eac-768a-4b57-b246-d467d0a0932e/result.txt -w /tmp/biobb/unitests_167/pmxanalyse/sandbox_255a2eac-768a-4b57-b246-d467d0a0932e/plot.png -m CGI BAR JARZ -t 298.15 -n 1 --skip 1 --prec 2 --units kJ --nbins 20 --dpi 600\n\n2024-06-14 18:47:04,846 [MainThread  ] [INFO ]  Exit code 0\n\n2024-06-14 18:47:04,847 [MainThread  ] [INFO ]  \n\n ========================================================\n                   PROCESSING THE DATA\n ========================================================\n  Forward Data\n    First accepted file: 92c0201c-6e07-42ab-a977-d62b22b762d5/frame0/dhdl0.xvg\n    # data points: 25001\n    Length of trajectory:   50.000 ps\n    Delta lambda:  0.00004\n\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame1/dhdl1.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame2/dhdl2.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame3/dhdl3.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame4/dhdl4.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame5/dhdl5.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame6/dhdl6.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame7/dhdl7.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame8/dhdl8.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame9/dhdl9.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame10/dhdl10.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame11/dhdl11.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame12/dhdl12.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame13/dhdl13.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame14/dhdl14.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame15/dhdl15.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame16/dhdl16.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame17/dhdl17.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame18/dhdl18.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame19/dhdl19.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame20/dhdl20.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame21/dhdl21.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame22/dhdl22.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame23/dhdl23.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame24/dhdl24.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame25/dhdl25.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame26/dhdl26.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame27/dhdl27.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame28/dhdl28.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame29/dhdl29.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame30/dhdl30.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame31/dhdl31.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame32/dhdl32.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame33/dhdl33.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame34/dhdl34.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame35/dhdl35.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame36/dhdl36.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame37/dhdl37.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame38/dhdl38.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame39/dhdl39.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame40/dhdl40.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame41/dhdl41.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame42/dhdl42.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame43/dhdl43.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame44/dhdl44.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame45/dhdl45.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame46/dhdl46.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame47/dhdl47.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame48/dhdl48.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame49/dhdl49.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame50/dhdl50.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame51/dhdl51.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame52/dhdl52.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame53/dhdl53.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame54/dhdl54.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame55/dhdl55.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame56/dhdl56.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame57/dhdl57.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame58/dhdl58.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame59/dhdl59.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame60/dhdl60.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame61/dhdl61.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame62/dhdl62.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame63/dhdl63.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame64/dhdl64.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame65/dhdl65.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame66/dhdl66.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame67/dhdl67.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame68/dhdl68.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame69/dhdl69.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame70/dhdl70.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame71/dhdl71.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame72/dhdl72.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame73/dhdl73.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame74/dhdl74.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame75/dhdl75.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame76/dhdl76.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame77/dhdl77.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame78/dhdl78.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame79/dhdl79.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame80/dhdl80.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame81/dhdl81.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame82/dhdl82.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame83/dhdl83.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame84/dhdl84.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame85/dhdl85.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame86/dhdl86.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame87/dhdl87.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame88/dhdl88.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame89/dhdl89.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame90/dhdl90.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame91/dhdl91.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame92/dhdl92.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame93/dhdl93.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame94/dhdl94.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame95/dhdl95.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame96/dhdl96.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame97/dhdl97.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame98/dhdl98.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame99/dhdl99.xvg\n\n  Reverse Data\n    First accepted file: 80a21ac4-5be8-4864-aa0e-91cbea071493/frame0/dhdl0.xvg\n    # data points: 25001\n    Length of trajectory:   50.000 ps\n    Delta lambda: -0.00004\n\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame1/dhdl1.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame2/dhdl2.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame3/dhdl3.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame4/dhdl4.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame5/dhdl5.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame6/dhdl6.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame7/dhdl7.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame8/dhdl8.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame9/dhdl9.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame10/dhdl10.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame11/dhdl11.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame12/dhdl12.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame13/dhdl13.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame14/dhdl14.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame15/dhdl15.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame16/dhdl16.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame17/dhdl17.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame18/dhdl18.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame19/dhdl19.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame20/dhdl20.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame21/dhdl21.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame22/dhdl22.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame23/dhdl23.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame24/dhdl24.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame25/dhdl25.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame26/dhdl26.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame27/dhdl27.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame28/dhdl28.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame29/dhdl29.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame30/dhdl30.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame31/dhdl31.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame32/dhdl32.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame33/dhdl33.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame34/dhdl34.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame35/dhdl35.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame36/dhdl36.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame37/dhdl37.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame38/dhdl38.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame39/dhdl39.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame40/dhdl40.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame41/dhdl41.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame42/dhdl42.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame43/dhdl43.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame44/dhdl44.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame45/dhdl45.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame46/dhdl46.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame47/dhdl47.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame48/dhdl48.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame49/dhdl49.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame50/dhdl50.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame51/dhdl51.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame52/dhdl52.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame53/dhdl53.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame54/dhdl54.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame55/dhdl55.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame56/dhdl56.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame57/dhdl57.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame58/dhdl58.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame59/dhdl59.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame60/dhdl60.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame61/dhdl61.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame62/dhdl62.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame63/dhdl63.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame64/dhdl64.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame65/dhdl65.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame66/dhdl66.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame67/dhdl67.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame68/dhdl68.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame69/dhdl69.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame70/dhdl70.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame71/dhdl71.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame72/dhdl72.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame73/dhdl73.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame74/dhdl74.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame75/dhdl75.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame76/dhdl76.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame77/dhdl77.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame78/dhdl78.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame79/dhdl79.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame80/dhdl80.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame81/dhdl81.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame82/dhdl82.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame83/dhdl83.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame84/dhdl84.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame85/dhdl85.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame86/dhdl86.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame87/dhdl87.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame88/dhdl88.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame89/dhdl89.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame90/dhdl90.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame91/dhdl91.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame92/dhdl92.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame93/dhdl93.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame94/dhdl94.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame95/dhdl95.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame96/dhdl96.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame97/dhdl97.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame98/dhdl98.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/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  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dG =     8.39 kJ/mol\n  CGI: Std Err (bootstrap:parametric) =     0.40 kJ/mol\n  CGI: Std Err (bootstrap) =     0.41 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 9/100\r  Bootstrap (Std Err): iteration 10/100\r  Bootstrap (Std Err): iteration 11/100\r  Bootstrap (Std Err): iteration 12/100\r  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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) =     3.08 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  Bootstrap (Std Err): iteration 17/100\r  Bootstrap (Std Err): iteration 18/100\r  Bootstrap (Std Err): iteration 19/100\r  Bootstrap 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41/100\r  Bootstrap (Std Err): iteration 42/100\r  Bootstrap (Std Err): iteration 43/100\r  Bootstrap (Std Err): iteration 44/100\r  Bootstrap (Std Err): iteration 45/100\r  Bootstrap (Std Err): iteration 46/100\r  Bootstrap (Std Err): iteration 47/100\r  Bootstrap (Std Err): iteration 48/100\r  Bootstrap (Std Err): iteration 49/100\r  Bootstrap (Std Err): iteration 50/100\r  Bootstrap (Std Err): iteration 51/100\r  Bootstrap (Std Err): iteration 52/100\r  Bootstrap (Std Err): iteration 53/100\r  Bootstrap (Std Err): iteration 54/100\r  Bootstrap (Std Err): iteration 55/100\r  Bootstrap (Std Err): iteration 56/100\r  Bootstrap (Std Err): iteration 57/100\r  Bootstrap (Std Err): iteration 58/100\r  Bootstrap (Std Err): iteration 59/100\r  Bootstrap (Std Err): iteration 60/100\r  Bootstrap (Std Err): iteration 61/100\r  Bootstrap (Std Err): iteration 62/100\r  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) =     0.60 kJ/mol\n  JARZ_Gauss: Std Err Reverse (bootstrap) =     2.78 kJ/mol\n ========================================================\n\n   Plotting histograms......\n\n   ......done...........\n\n   Execution time = 00:00:11\n\n\n2024-06-14 18:47:04,873 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80a21ac4-5be8-4864-aa0e-91cbea071493/frame81/dhdl81.xvg 80a21ac4-5be8-4864-aa0e-91cbea071493/frame82/dhdl82.xvg 80a21ac4-5be8-4864-aa0e-91cbea071493/frame83/dhdl83.xvg 80a21ac4-5be8-4864-aa0e-91cbea071493/frame84/dhdl84.xvg 80a21ac4-5be8-4864-aa0e-91cbea071493/frame85/dhdl85.xvg 80a21ac4-5be8-4864-aa0e-91cbea071493/frame86/dhdl86.xvg 80a21ac4-5be8-4864-aa0e-91cbea071493/frame87/dhdl87.xvg 80a21ac4-5be8-4864-aa0e-91cbea071493/frame88/dhdl88.xvg 80a21ac4-5be8-4864-aa0e-91cbea071493/frame89/dhdl89.xvg 80a21ac4-5be8-4864-aa0e-91cbea071493/frame9/dhdl9.xvg 80a21ac4-5be8-4864-aa0e-91cbea071493/frame90/dhdl90.xvg 80a21ac4-5be8-4864-aa0e-91cbea071493/frame91/dhdl91.xvg 80a21ac4-5be8-4864-aa0e-91cbea071493/frame92/dhdl92.xvg 80a21ac4-5be8-4864-aa0e-91cbea071493/frame93/dhdl93.xvg 80a21ac4-5be8-4864-aa0e-91cbea071493/frame94/dhdl94.xvg 80a21ac4-5be8-4864-aa0e-91cbea071493/frame95/dhdl95.xvg 80a21ac4-5be8-4864-aa0e-91cbea071493/frame96/dhdl96.xvg 80a21ac4-5be8-4864-aa0e-91cbea071493/frame97/dhdl97.xvg 80a21ac4-5be8-4864-aa0e-91cbea071493/frame98/dhdl98.xvg 80a21ac4-5be8-4864-aa0e-91cbea071493/frame99/dhdl99.xvg -o /tmp/biobb/unitests_167/pmxanalyse/sandbox_255a2eac-768a-4b57-b246-d467d0a0932e/result.txt -w /tmp/biobb/unitests_167/pmxanalyse/sandbox_255a2eac-768a-4b57-b246-d467d0a0932e/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_167/pmxanalyse/pmxanalyse_log.out:cmd_wrapper.py:50 Exit code 0\n\nINFO     /tmp/biobb/unitests_167/pmxanalyse/pmxanalyse_log.out:cmd_wrapper.py:52 \n\n ========================================================\n                   PROCESSING THE DATA\n ========================================================\n  Forward Data\n    First accepted file: 92c0201c-6e07-42ab-a977-d62b22b762d5/frame0/dhdl0.xvg\n    # data points: 25001\n    Length of trajectory:   50.000 ps\n    Delta lambda:  0.00004\n\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame1/dhdl1.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame2/dhdl2.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame3/dhdl3.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame4/dhdl4.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame5/dhdl5.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame6/dhdl6.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame7/dhdl7.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame8/dhdl8.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame9/dhdl9.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame10/dhdl10.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame11/dhdl11.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame12/dhdl12.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame13/dhdl13.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame14/dhdl14.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame15/dhdl15.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame16/dhdl16.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame17/dhdl17.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame18/dhdl18.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame19/dhdl19.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame20/dhdl20.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame21/dhdl21.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame22/dhdl22.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame23/dhdl23.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame24/dhdl24.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame25/dhdl25.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame26/dhdl26.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame27/dhdl27.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame28/dhdl28.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame29/dhdl29.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame30/dhdl30.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame31/dhdl31.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame32/dhdl32.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame33/dhdl33.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame34/dhdl34.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame35/dhdl35.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame36/dhdl36.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame37/dhdl37.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame38/dhdl38.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame39/dhdl39.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame40/dhdl40.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame41/dhdl41.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame42/dhdl42.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame43/dhdl43.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame44/dhdl44.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame45/dhdl45.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame46/dhdl46.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame47/dhdl47.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame48/dhdl48.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame49/dhdl49.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame50/dhdl50.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame51/dhdl51.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame52/dhdl52.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame53/dhdl53.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame54/dhdl54.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame55/dhdl55.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame56/dhdl56.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame57/dhdl57.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame58/dhdl58.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame59/dhdl59.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame60/dhdl60.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame61/dhdl61.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame62/dhdl62.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame63/dhdl63.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame64/dhdl64.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame65/dhdl65.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame66/dhdl66.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame67/dhdl67.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame68/dhdl68.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame69/dhdl69.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame70/dhdl70.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame71/dhdl71.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame72/dhdl72.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame73/dhdl73.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame74/dhdl74.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame75/dhdl75.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame76/dhdl76.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame77/dhdl77.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame78/dhdl78.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame79/dhdl79.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame80/dhdl80.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame81/dhdl81.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame82/dhdl82.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame83/dhdl83.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame84/dhdl84.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame85/dhdl85.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame86/dhdl86.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame87/dhdl87.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame88/dhdl88.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame89/dhdl89.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame90/dhdl90.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame91/dhdl91.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame92/dhdl92.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame93/dhdl93.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame94/dhdl94.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame95/dhdl95.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame96/dhdl96.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame97/dhdl97.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame98/dhdl98.xvg\r    Reading 92c0201c-6e07-42ab-a977-d62b22b762d5/frame99/dhdl99.xvg\n\n  Reverse Data\n    First accepted file: 80a21ac4-5be8-4864-aa0e-91cbea071493/frame0/dhdl0.xvg\n    # data points: 25001\n    Length of trajectory:   50.000 ps\n    Delta lambda: -0.00004\n\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame1/dhdl1.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame2/dhdl2.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame3/dhdl3.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame4/dhdl4.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame5/dhdl5.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame6/dhdl6.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame7/dhdl7.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame8/dhdl8.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame9/dhdl9.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame10/dhdl10.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame11/dhdl11.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame12/dhdl12.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame13/dhdl13.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame14/dhdl14.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame15/dhdl15.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame16/dhdl16.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame17/dhdl17.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame18/dhdl18.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame19/dhdl19.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame20/dhdl20.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame21/dhdl21.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame22/dhdl22.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame23/dhdl23.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame24/dhdl24.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame25/dhdl25.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame26/dhdl26.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame27/dhdl27.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame28/dhdl28.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame29/dhdl29.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame30/dhdl30.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame31/dhdl31.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame32/dhdl32.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame33/dhdl33.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame34/dhdl34.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame35/dhdl35.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame36/dhdl36.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame37/dhdl37.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame38/dhdl38.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame39/dhdl39.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame40/dhdl40.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame41/dhdl41.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame42/dhdl42.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame43/dhdl43.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame44/dhdl44.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame45/dhdl45.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame46/dhdl46.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame47/dhdl47.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame48/dhdl48.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame49/dhdl49.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame50/dhdl50.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame51/dhdl51.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame52/dhdl52.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame53/dhdl53.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame54/dhdl54.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame55/dhdl55.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame56/dhdl56.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame57/dhdl57.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame58/dhdl58.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame59/dhdl59.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame60/dhdl60.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame61/dhdl61.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame62/dhdl62.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame63/dhdl63.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame64/dhdl64.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame65/dhdl65.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame66/dhdl66.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame67/dhdl67.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame68/dhdl68.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame69/dhdl69.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame70/dhdl70.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame71/dhdl71.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame72/dhdl72.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame73/dhdl73.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame74/dhdl74.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame75/dhdl75.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame76/dhdl76.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame77/dhdl77.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame78/dhdl78.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame79/dhdl79.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame80/dhdl80.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame81/dhdl81.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame82/dhdl82.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame83/dhdl83.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame84/dhdl84.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame85/dhdl85.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame86/dhdl86.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame87/dhdl87.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame88/dhdl88.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame89/dhdl89.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame90/dhdl90.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame91/dhdl91.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame92/dhdl92.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame93/dhdl93.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame94/dhdl94.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame95/dhdl95.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame96/dhdl96.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame97/dhdl97.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/frame98/dhdl98.xvg\r    Reading 80a21ac4-5be8-4864-aa0e-91cbea071493/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  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dG =     8.39 kJ/mol\n  CGI: Std Err (bootstrap:parametric) =     0.40 kJ/mol\n  CGI: Std Err (bootstrap) =     0.41 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 9/100\r  Bootstrap (Std Err): iteration 10/100\r  Bootstrap (Std Err): iteration 11/100\r  Bootstrap (Std Err): iteration 12/100\r  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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) =     3.08 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  Bootstrap (Std Err): iteration 17/100\r  Bootstrap (Std Err): iteration 18/100\r  Bootstrap (Std Err): iteration 19/100\r  Bootstrap 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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) =     0.60 kJ/mol\n  JARZ_Gauss: Std Err Reverse (bootstrap) =     2.78 kJ/mol\n ========================================================\n\n   Plotting histograms......\n\n   ......done...........\n\n   Execution time = 00:00:11\n\n\nINFO     /tmp/biobb/unitests_167/pmxanalyse/pmxanalyse_log.out:file_utils.py:391 Removed: [&amp;#x27;/tmp/biobb/unitests_167/pmxanalyse/sandbox_255a2eac-768a-4b57-b246-d467d0a0932e&amp;#x27;, &amp;#x27;92c0201c-6e07-42ab-a977-d62b22b762d5&amp;#x27;, &amp;#x27;80a21ac4-5be8-4864-aa0e-91cbea071493&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_167\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;00:00:04&#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;00:00:04&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-06-14 18:47:05,528 [MainThread  ] [INFO ]  Executing biobb_pmx.pmxbiobb.pmxatom_mapping Version: 4.2.1\n2024-06-14 18:47:05,528 [MainThread  ] [INFO ]  /tmp/biobb/unitests_167/pmxatom_mapping/sandbox_54a3d2a7-a4fa-4b98-98e3-eaa65029f514 directory successfully created\n2024-06-14 18:47:05,528 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/lig1.pdb to /tmp/biobb/unitests_167/pmxatom_mapping/sandbox_54a3d2a7-a4fa-4b98-98e3-eaa65029f514\n2024-06-14 18:47:05,528 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/lig2.pdb to /tmp/biobb/unitests_167/pmxatom_mapping/sandbox_54a3d2a7-a4fa-4b98-98e3-eaa65029f514\n2024-06-14 18:47:05,529 [MainThread  ] [INFO ]  pmx atomMapping -i1 /tmp/biobb/unitests_167/pmxatom_mapping/sandbox_54a3d2a7-a4fa-4b98-98e3-eaa65029f514/lig1.pdb -i2 /tmp/biobb/unitests_167/pmxatom_mapping/sandbox_54a3d2a7-a4fa-4b98-98e3-eaa65029f514/lig2.pdb -o1 /tmp/biobb/unitests_167/pmxatom_mapping/sandbox_54a3d2a7-a4fa-4b98-98e3-eaa65029f514/pairs1.dat -o2 /tmp/biobb/unitests_167/pmxatom_mapping/sandbox_54a3d2a7-a4fa-4b98-98e3-eaa65029f514/pairs2.dat -log /tmp/biobb/unitests_167/pmxatom_mapping/sandbox_54a3d2a7-a4fa-4b98-98e3-eaa65029f514/atom_mapping.log --d 0.05\n\n2024-06-14 18:47:09,879 [MainThread  ] [INFO ]  Exit code 0\n\n2024-06-14 18:47:09,879 [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\n2024-06-14 18:47:09,880 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_167/pmxatom_mapping/sandbox_54a3d2a7-a4fa-4b98-98e3-eaa65029f514&amp;#x27;]\nChecking if empty file: /tmp/biobb/unitests_167/pmxatom_mapping/pairs1.dat\nChecking if empty file: /tmp/biobb/unitests_167/pmxatom_mapping/pairs2.dat\nComparing: \n        File_A: /tmp/biobb/unitests_167/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_167/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_167/pmxatom_mapping/pmxatom_mapping_log.out:file_utils.py:391 Executing biobb_pmx.pmxbiobb.pmxatom_mapping Version: 4.2.1\nINFO     /tmp/biobb/unitests_167/pmxatom_mapping/pmxatom_mapping_log.out:file_utils.py:82 /tmp/biobb/unitests_167/pmxatom_mapping/sandbox_54a3d2a7-a4fa-4b98-98e3-eaa65029f514 directory successfully created\nINFO     /tmp/biobb/unitests_167/pmxatom_mapping/pmxatom_mapping_log.out:file_utils.py:391 Copy: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/lig1.pdb to /tmp/biobb/unitests_167/pmxatom_mapping/sandbox_54a3d2a7-a4fa-4b98-98e3-eaa65029f514\nINFO     /tmp/biobb/unitests_167/pmxatom_mapping/pmxatom_mapping_log.out:file_utils.py:391 Copy: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/lig2.pdb to /tmp/biobb/unitests_167/pmxatom_mapping/sandbox_54a3d2a7-a4fa-4b98-98e3-eaa65029f514\nINFO     /tmp/biobb/unitests_167/pmxatom_mapping/pmxatom_mapping_log.out:cmd_wrapper.py:33 pmx atomMapping -i1 /tmp/biobb/unitests_167/pmxatom_mapping/sandbox_54a3d2a7-a4fa-4b98-98e3-eaa65029f514/lig1.pdb -i2 /tmp/biobb/unitests_167/pmxatom_mapping/sandbox_54a3d2a7-a4fa-4b98-98e3-eaa65029f514/lig2.pdb -o1 /tmp/biobb/unitests_167/pmxatom_mapping/sandbox_54a3d2a7-a4fa-4b98-98e3-eaa65029f514/pairs1.dat -o2 /tmp/biobb/unitests_167/pmxatom_mapping/sandbox_54a3d2a7-a4fa-4b98-98e3-eaa65029f514/pairs2.dat -log /tmp/biobb/unitests_167/pmxatom_mapping/sandbox_54a3d2a7-a4fa-4b98-98e3-eaa65029f514/atom_mapping.log --d 0.05\n\nINFO     /tmp/biobb/unitests_167/pmxatom_mapping/pmxatom_mapping_log.out:cmd_wrapper.py:50 Exit code 0\n\nINFO     /tmp/biobb/unitests_167/pmxatom_mapping/pmxatom_mapping_log.out:cmd_wrapper.py:52 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_167/pmxatom_mapping/pmxatom_mapping_log.out:file_utils.py:391 Removed: [&amp;#x27;/tmp/biobb/unitests_167/pmxatom_mapping/sandbox_54a3d2a7-a4fa-4b98-98e3-eaa65029f514&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_167\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;45 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;45 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 -----------------------------\n2024-06-14 18:47:09,918 [MainThread  ] [INFO ]  Executing biobb_pmx.pmxbiobb.pmxcreate_top Version: 4.2.1\n2024-06-14 18:47:09,918 [MainThread  ] [INFO ]  /tmp/biobb/unitests_167/pmxcreate_top/sandbox_f66b0f7b-b379-4b6a-90b4-3d8ede9079ee directory successfully created\n2024-06-14 18:47:09,918 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/topo1.itp to /tmp/biobb/unitests_167/pmxcreate_top/sandbox_f66b0f7b-b379-4b6a-90b4-3d8ede9079ee\n2024-06-14 18:47:09,919 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/topo2.itp to /tmp/biobb/unitests_167/pmxcreate_top/sandbox_f66b0f7b-b379-4b6a-90b4-3d8ede9079ee\n2024-06-14 18:47:09,919 [MainThread  ] [INFO ]  Running create_top from pmx package...\n\n2024-06-14 18:47:09,919 [MainThread  ] [INFO ]  Creating a818eec5-f0b4-4084-8851-bca83fd3357c temporary folder\n2024-06-14 18:47:09,919 [MainThread  ] [INFO ]  Creating topo1.itp itp file in temporary folder\n2024-06-14 18:47:09,919 [MainThread  ] [INFO ]  Creating topo2.itp itp file in temporary folder\n2024-06-14 18:47:09,920 [MainThread  ] [INFO ]  Compressing topology to: /tmp/biobb/unitests_167/pmxcreate_top/topo.zip\n2024-06-14 18:47:09,920 [MainThread  ] [INFO ]  Ignored file amber99sb-star-ildn-mut.ff/forcefield.itp\n2024-06-14 18:47:09,921 [MainThread  ] [INFO ]  Ignored file amber99sb-star-ildn-mut.ff/spce.itp\n2024-06-14 18:47:09,921 [MainThread  ] [INFO ]  Ignored file amber99sb-star-ildn-mut.ff/ions.itp\n2024-06-14 18:47:09,922 [MainThread  ] [INFO ]  Adding:\n2024-06-14 18:47:09,922 [MainThread  ] [INFO ]  [&amp;#x27;topo1.itp&amp;#x27;, &amp;#x27;topo2.itp&amp;#x27;, &amp;#x27;topology.top&amp;#x27;]\n2024-06-14 18:47:09,922 [MainThread  ] [INFO ]  to: /tmp/biobb/unitests_167/pmxcreate_top/topo.zip\n2024-06-14 18:47:09,922 [MainThread  ] [INFO ]  Removed: [&amp;#x27;topo1.itp&amp;#x27;, &amp;#x27;topo2.itp&amp;#x27;, &amp;#x27;topology.top&amp;#x27;]\n2024-06-14 18:47:09,922 [MainThread  ] [INFO ]  Exit code 0\n\n2024-06-14 18:47:09,922 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_167/pmxcreate_top/sandbox_f66b0f7b-b379-4b6a-90b4-3d8ede9079ee&amp;#x27;]\nChecking if empty file: /tmp/biobb/unitests_167/pmxcreate_top/topo.zip\nThis is a ZIP comparison!\nUnzipping:\nCreating a unique_dir for: /tmp/biobb/unitests_167/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: e54b7e33-ca35-42f9-88d8-cb9b532bb723/topo1.itp\n     FILE_B: cff13908-9656-46c0-bf4b-ebc73b4bb7d4/topo1.itp\nComparing TOP/ITP:\n     FILE_A: e54b7e33-ca35-42f9-88d8-cb9b532bb723/topo2.itp\n     FILE_B: cff13908-9656-46c0-bf4b-ebc73b4bb7d4/topo2.itp\nComparing TOP/ITP:\n     FILE_A: e54b7e33-ca35-42f9-88d8-cb9b532bb723/topology.top\n     FILE_B: cff13908-9656-46c0-bf4b-ebc73b4bb7d4/topology.top\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_167/pmxcreate_top/pmxcreate_top_log.out:file_utils.py:391 Executing biobb_pmx.pmxbiobb.pmxcreate_top Version: 4.2.1\nINFO     /tmp/biobb/unitests_167/pmxcreate_top/pmxcreate_top_log.out:file_utils.py:82 /tmp/biobb/unitests_167/pmxcreate_top/sandbox_f66b0f7b-b379-4b6a-90b4-3d8ede9079ee directory successfully created\nINFO     /tmp/biobb/unitests_167/pmxcreate_top/pmxcreate_top_log.out:file_utils.py:391 Copy: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/topo1.itp to /tmp/biobb/unitests_167/pmxcreate_top/sandbox_f66b0f7b-b379-4b6a-90b4-3d8ede9079ee\nINFO     /tmp/biobb/unitests_167/pmxcreate_top/pmxcreate_top_log.out:file_utils.py:391 Copy: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/topo2.itp to /tmp/biobb/unitests_167/pmxcreate_top/sandbox_f66b0f7b-b379-4b6a-90b4-3d8ede9079ee\nINFO     /tmp/biobb/unitests_167/pmxcreate_top/pmxcreate_top_log.out:file_utils.py:391 Running create_top from pmx package...\n\nINFO     /tmp/biobb/unitests_167/pmxcreate_top/pmxcreate_top_log.out:file_utils.py:391 Creating a818eec5-f0b4-4084-8851-bca83fd3357c temporary folder\nINFO     /tmp/biobb/unitests_167/pmxcreate_top/pmxcreate_top_log.out:file_utils.py:391 Creating topo1.itp itp file in temporary folder\nINFO     /tmp/biobb/unitests_167/pmxcreate_top/pmxcreate_top_log.out:file_utils.py:391 Creating topo2.itp itp file in temporary folder\nINFO     /tmp/biobb/unitests_167/pmxcreate_top/pmxcreate_top_log.out:file_utils.py:391 Compressing topology to: /tmp/biobb/unitests_167/pmxcreate_top/topo.zip\nINFO     /tmp/biobb/unitests_167/pmxcreate_top/pmxcreate_top_log.out:file_utils.py:203 Ignored file amber99sb-star-ildn-mut.ff/forcefield.itp\nINFO     /tmp/biobb/unitests_167/pmxcreate_top/pmxcreate_top_log.out:file_utils.py:203 Ignored file amber99sb-star-ildn-mut.ff/spce.itp\nINFO     /tmp/biobb/unitests_167/pmxcreate_top/pmxcreate_top_log.out:file_utils.py:203 Ignored file amber99sb-star-ildn-mut.ff/ions.itp\nINFO     /tmp/biobb/unitests_167/pmxcreate_top/pmxcreate_top_log.out:file_utils.py:148 Adding:\nINFO     /tmp/biobb/unitests_167/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_167/pmxcreate_top/pmxcreate_top_log.out:file_utils.py:150 to: /tmp/biobb/unitests_167/pmxcreate_top/topo.zip\nINFO     /tmp/biobb/unitests_167/pmxcreate_top/pmxcreate_top_log.out:file_utils.py:391 Removed: [&amp;#x27;topo1.itp&amp;#x27;, &amp;#x27;topo2.itp&amp;#x27;, &amp;#x27;topology.top&amp;#x27;]\nINFO     /tmp/biobb/unitests_167/pmxcreate_top/pmxcreate_top_log.out:file_utils.py:391 Exit code 0\n\nINFO     /tmp/biobb/unitests_167/pmxcreate_top/pmxcreate_top_log.out:file_utils.py:391 Removed: [&amp;#x27;/tmp/biobb/unitests_167/pmxcreate_top/sandbox_f66b0f7b-b379-4b6a-90b4-3d8ede9079ee&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_167\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;00:00:09&#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;00:00:09&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-06-14 18:47:09,962 [MainThread  ] [INFO ]  Executing biobb_pmx.pmxbiobb.pmxgentop Version: 4.2.1\n2024-06-14 18:47:09,962 [MainThread  ] [INFO ]  /tmp/biobb/unitests_167/pmxgentop/sandbox_f8f88e99-1881-4ce3-ab08-09fe5c1f2e4e directory successfully created\n2024-06-14 18:47:09,964 [MainThread  ] [INFO ]  Extracting: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/mut_gmx.top.zip\n2024-06-14 18:47:09,965 [MainThread  ] [INFO ]  to:\n2024-06-14 18:47:09,965 [MainThread  ] [INFO ]  [&amp;#x27;9d760abe-e3ee-44e4-8f35-4061dbb9985d/p2g.top&amp;#x27;, &amp;#x27;9d760abe-e3ee-44e4-8f35-4061dbb9985d/p2g_Ion.itp&amp;#x27;, &amp;#x27;9d760abe-e3ee-44e4-8f35-4061dbb9985d/p2g_Protein_chain_A.itp&amp;#x27;, &amp;#x27;9d760abe-e3ee-44e4-8f35-4061dbb9985d/posre_Ion.itp&amp;#x27;, &amp;#x27;9d760abe-e3ee-44e4-8f35-4061dbb9985d/posre_Protein_chain_A.itp&amp;#x27;]\n2024-06-14 18:47:09,965 [MainThread  ] [INFO ]  Unzipping: \n2024-06-14 18:47:09,965 [MainThread  ] [INFO ]  /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/mut_gmx.top.zip\n2024-06-14 18:47:09,965 [MainThread  ] [INFO ]  To: \n2024-06-14 18:47:09,965 [MainThread  ] [INFO ]  9d760abe-e3ee-44e4-8f35-4061dbb9985d/p2g.top\n2024-06-14 18:47:09,965 [MainThread  ] [INFO ]  9d760abe-e3ee-44e4-8f35-4061dbb9985d/p2g_Ion.itp\n2024-06-14 18:47:09,965 [MainThread  ] [INFO ]  9d760abe-e3ee-44e4-8f35-4061dbb9985d/p2g_Protein_chain_A.itp\n2024-06-14 18:47:09,965 [MainThread  ] [INFO ]  9d760abe-e3ee-44e4-8f35-4061dbb9985d/posre_Ion.itp\n2024-06-14 18:47:09,965 [MainThread  ] [INFO ]  9d760abe-e3ee-44e4-8f35-4061dbb9985d/posre_Protein_chain_A.itp\n2024-06-14 18:47:09,965 [MainThread  ] [INFO ]  unique_dir_output_file: a9b948e3-a2c0-4044-b131-9072f679a0d0/pmxgentop_p2g.top\n2024-06-14 18:47:09,965 [MainThread  ] [INFO ]  pmx gentop -o a9b948e3-a2c0-4044-b131-9072f679a0d0/pmxgentop_p2g.top -ff amber99sb-star-ildn-mut -p 9d760abe-e3ee-44e4-8f35-4061dbb9985d/p2g.top\n\n2024-06-14 18:47:18,255 [MainThread  ] [INFO ]  Exit code 0\n\n2024-06-14 18:47:18,255 [MainThread  ] [INFO ]  \nlog_&amp;gt; Reading input top file &amp;quot;9d760abe-e3ee-44e4-8f35-4061dbb9985d/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_167/pmxgentop/a9b948e3-a2c0-4044-b131-9072f679a0d0/pmx_p2g_Protein_chain_A.itp&amp;quot;&amp;quot;\n\nlog_&amp;gt; Writing itp file &amp;quot;/tmp/biobb/unitests_167/pmxgentop/a9b948e3-a2c0-4044-b131-9072f679a0d0/pmx_p2g_Ion.itp&amp;quot;&amp;quot;\n\nlog_&amp;gt; Writing topology file &amp;quot;a9b948e3-a2c0-4044-b131-9072f679a0d0/pmxgentop_p2g.top&amp;quot;&amp;quot;\n\nb-states filled...........\n\n\n2024-06-14 18:47:18,867 [MainThread  ] [INFO ]  Check if a9b948e3-a2c0-4044-b131-9072f679a0d0/p2g_Protein_chain_A.itp exists\n2024-06-14 18:47:18,868 [MainThread  ] [INFO ]  Copying 9d760abe-e3ee-44e4-8f35-4061dbb9985d/p2g_Protein_chain_A.itp to: a9b948e3-a2c0-4044-b131-9072f679a0d0\n2024-06-14 18:47:18,868 [MainThread  ] [INFO ]  Check if a9b948e3-a2c0-4044-b131-9072f679a0d0/p2g_Ion.itp exists\n2024-06-14 18:47:18,868 [MainThread  ] [INFO ]  Copying 9d760abe-e3ee-44e4-8f35-4061dbb9985d/p2g_Ion.itp to: a9b948e3-a2c0-4044-b131-9072f679a0d0\n2024-06-14 18:47:18,868 [MainThread  ] [INFO ]  Check if a9b948e3-a2c0-4044-b131-9072f679a0d0/p2g.top exists\n2024-06-14 18:47:18,869 [MainThread  ] [INFO ]  Copying 9d760abe-e3ee-44e4-8f35-4061dbb9985d/p2g.top to: a9b948e3-a2c0-4044-b131-9072f679a0d0\n2024-06-14 18:47:18,869 [MainThread  ] [INFO ]  Check if a9b948e3-a2c0-4044-b131-9072f679a0d0/posre_Protein_chain_A.itp exists\n2024-06-14 18:47:18,869 [MainThread  ] [INFO ]  Copying 9d760abe-e3ee-44e4-8f35-4061dbb9985d/posre_Protein_chain_A.itp to: a9b948e3-a2c0-4044-b131-9072f679a0d0\n2024-06-14 18:47:18,869 [MainThread  ] [INFO ]  Check if a9b948e3-a2c0-4044-b131-9072f679a0d0/posre_Ion.itp exists\n2024-06-14 18:47:18,869 [MainThread  ] [INFO ]  Copying 9d760abe-e3ee-44e4-8f35-4061dbb9985d/posre_Ion.itp to: a9b948e3-a2c0-4044-b131-9072f679a0d0\n2024-06-14 18:47:18,869 [MainThread  ] [INFO ]  Compressing topology to: /tmp/biobb/unitests_167/pmxgentop/output_topology.zip\n2024-06-14 18:47:18,870 [MainThread  ] [INFO ]  Ignored file a9b948e3-a2c0-4044-b131-9072f679a0d0/amber99sb-star-ildn-mut.ff/forcefield.itp\n2024-06-14 18:47:18,879 [MainThread  ] [INFO ]  Ignored file a9b948e3-a2c0-4044-b131-9072f679a0d0/amber99sb-star-ildn-mut.ff/spce.itp\n2024-06-14 18:47:18,880 [MainThread  ] [INFO ]  Ignored file a9b948e3-a2c0-4044-b131-9072f679a0d0/amber99sb-star-ildn-mut.ff/ions.itp\n2024-06-14 18:47:18,882 [MainThread  ] [INFO ]  Adding:\n2024-06-14 18:47:18,882 [MainThread  ] [INFO ]  [&amp;#x27;a9b948e3-a2c0-4044-b131-9072f679a0d0/pmx_p2g_Ion.itp&amp;#x27;, &amp;#x27;a9b948e3-a2c0-4044-b131-9072f679a0d0/pmx_p2g_Protein_chain_A.itp&amp;#x27;, &amp;#x27;a9b948e3-a2c0-4044-b131-9072f679a0d0/pmxgentop_p2g.top&amp;#x27;, &amp;#x27;a9b948e3-a2c0-4044-b131-9072f679a0d0/posre_Ion.itp&amp;#x27;, &amp;#x27;a9b948e3-a2c0-4044-b131-9072f679a0d0/posre_Protein_chain_A.itp&amp;#x27;]\n2024-06-14 18:47:18,882 [MainThread  ] [INFO ]  to: /tmp/biobb/unitests_167/pmxgentop/output_topology.zip\n2024-06-14 18:47:18,919 [MainThread  ] [INFO ]  Removed: [&amp;#x27;a9b948e3-a2c0-4044-b131-9072f679a0d0/posre_Protein_chain_A.itp&amp;#x27;, &amp;#x27;a9b948e3-a2c0-4044-b131-9072f679a0d0/pmx_p2g_Protein_chain_A.itp&amp;#x27;, &amp;#x27;a9b948e3-a2c0-4044-b131-9072f679a0d0/posre_Ion.itp&amp;#x27;, &amp;#x27;a9b948e3-a2c0-4044-b131-9072f679a0d0/pmx_p2g_Ion.itp&amp;#x27;, &amp;#x27;a9b948e3-a2c0-4044-b131-9072f679a0d0/pmxgentop_p2g.top&amp;#x27;]\nChecking if empty file: /tmp/biobb/unitests_167/pmxgentop/output_topology.zip\nThis is a ZIP comparison!\nUnzipping:\nCreating a unique_dir for: /tmp/biobb/unitests_167/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: fd3b8a84-1cdf-450d-91af-56defd64a9c2/pmx_p2g_Ion.itp\n     FILE_B: 230abf13-ba3c-4f05-bd9f-0196660a22fe/pmx_p2g_Ion.itp\nComparing TOP/ITP:\n     FILE_A: fd3b8a84-1cdf-450d-91af-56defd64a9c2/pmx_p2g_Protein_chain_A.itp\n     FILE_B: 230abf13-ba3c-4f05-bd9f-0196660a22fe/pmx_p2g_Protein_chain_A.itp\nComparing TOP/ITP:\n     FILE_A: fd3b8a84-1cdf-450d-91af-56defd64a9c2/pmxgentop_p2g.top\n     FILE_B: 230abf13-ba3c-4f05-bd9f-0196660a22fe/pmxgentop_p2g.top\nComparing TOP/ITP:\n     FILE_A: fd3b8a84-1cdf-450d-91af-56defd64a9c2/posre_Ion.itp\n     FILE_B: 230abf13-ba3c-4f05-bd9f-0196660a22fe/posre_Ion.itp\nComparing TOP/ITP:\n     FILE_A: fd3b8a84-1cdf-450d-91af-56defd64a9c2/posre_Protein_chain_A.itp\n     FILE_B: 230abf13-ba3c-4f05-bd9f-0196660a22fe/posre_Protein_chain_A.itp\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_167/pmxgentop/pmxgentop_log.out:file_utils.py:391 Executing biobb_pmx.pmxbiobb.pmxgentop Version: 4.2.1\nINFO     /tmp/biobb/unitests_167/pmxgentop/pmxgentop_log.out:file_utils.py:82 /tmp/biobb/unitests_167/pmxgentop/sandbox_f8f88e99-1881-4ce3-ab08-09fe5c1f2e4e directory successfully created\nINFO     /tmp/biobb/unitests_167/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_167/pmxgentop/pmxgentop_log.out:file_utils.py:173 to:\nINFO     /tmp/biobb/unitests_167/pmxgentop/pmxgentop_log.out:file_utils.py:174 [&amp;#x27;9d760abe-e3ee-44e4-8f35-4061dbb9985d/p2g.top&amp;#x27;, &amp;#x27;9d760abe-e3ee-44e4-8f35-4061dbb9985d/p2g_Ion.itp&amp;#x27;, &amp;#x27;9d760abe-e3ee-44e4-8f35-4061dbb9985d/p2g_Protein_chain_A.itp&amp;#x27;, &amp;#x27;9d760abe-e3ee-44e4-8f35-4061dbb9985d/posre_Ion.itp&amp;#x27;, &amp;#x27;9d760abe-e3ee-44e4-8f35-4061dbb9985d/posre_Protein_chain_A.itp&amp;#x27;]\nINFO     /tmp/biobb/unitests_167/pmxgentop/pmxgentop_log.out:file_utils.py:252 Unzipping: \nINFO     /tmp/biobb/unitests_167/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_167/pmxgentop/pmxgentop_log.out:file_utils.py:254 To: \nINFO     /tmp/biobb/unitests_167/pmxgentop/pmxgentop_log.out:file_utils.py:256 9d760abe-e3ee-44e4-8f35-4061dbb9985d/p2g.top\nINFO     /tmp/biobb/unitests_167/pmxgentop/pmxgentop_log.out:file_utils.py:256 9d760abe-e3ee-44e4-8f35-4061dbb9985d/p2g_Ion.itp\nINFO     /tmp/biobb/unitests_167/pmxgentop/pmxgentop_log.out:file_utils.py:256 9d760abe-e3ee-44e4-8f35-4061dbb9985d/p2g_Protein_chain_A.itp\nINFO     /tmp/biobb/unitests_167/pmxgentop/pmxgentop_log.out:file_utils.py:256 9d760abe-e3ee-44e4-8f35-4061dbb9985d/posre_Ion.itp\nINFO     /tmp/biobb/unitests_167/pmxgentop/pmxgentop_log.out:file_utils.py:256 9d760abe-e3ee-44e4-8f35-4061dbb9985d/posre_Protein_chain_A.itp\nINFO     /tmp/biobb/unitests_167/pmxgentop/pmxgentop_log.out:file_utils.py:391 unique_dir_output_file: a9b948e3-a2c0-4044-b131-9072f679a0d0/pmxgentop_p2g.top\nINFO     /tmp/biobb/unitests_167/pmxgentop/pmxgentop_log.out:cmd_wrapper.py:33 pmx gentop -o a9b948e3-a2c0-4044-b131-9072f679a0d0/pmxgentop_p2g.top -ff amber99sb-star-ildn-mut -p 9d760abe-e3ee-44e4-8f35-4061dbb9985d/p2g.top\n\nINFO     /tmp/biobb/unitests_167/pmxgentop/pmxgentop_log.out:cmd_wrapper.py:50 Exit code 0\n\nINFO     /tmp/biobb/unitests_167/pmxgentop/pmxgentop_log.out:cmd_wrapper.py:52 \nlog_&amp;gt; Reading input top file &amp;quot;9d760abe-e3ee-44e4-8f35-4061dbb9985d/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_167/pmxgentop/a9b948e3-a2c0-4044-b131-9072f679a0d0/pmx_p2g_Protein_chain_A.itp&amp;quot;&amp;quot;\n\nlog_&amp;gt; Writing itp file &amp;quot;/tmp/biobb/unitests_167/pmxgentop/a9b948e3-a2c0-4044-b131-9072f679a0d0/pmx_p2g_Ion.itp&amp;quot;&amp;quot;\n\nlog_&amp;gt; Writing topology file &amp;quot;a9b948e3-a2c0-4044-b131-9072f679a0d0/pmxgentop_p2g.top&amp;quot;&amp;quot;\n\nb-states filled...........\n\n\nINFO     /tmp/biobb/unitests_167/pmxgentop/pmxgentop_log.out:file_utils.py:391 Check if a9b948e3-a2c0-4044-b131-9072f679a0d0/p2g_Protein_chain_A.itp exists\nINFO     /tmp/biobb/unitests_167/pmxgentop/pmxgentop_log.out:file_utils.py:391 Copying 9d760abe-e3ee-44e4-8f35-4061dbb9985d/p2g_Protein_chain_A.itp to: a9b948e3-a2c0-4044-b131-9072f679a0d0\nINFO     /tmp/biobb/unitests_167/pmxgentop/pmxgentop_log.out:file_utils.py:391 Check if a9b948e3-a2c0-4044-b131-9072f679a0d0/p2g_Ion.itp exists\nINFO     /tmp/biobb/unitests_167/pmxgentop/pmxgentop_log.out:file_utils.py:391 Copying 9d760abe-e3ee-44e4-8f35-4061dbb9985d/p2g_Ion.itp to: a9b948e3-a2c0-4044-b131-9072f679a0d0\nINFO     /tmp/biobb/unitests_167/pmxgentop/pmxgentop_log.out:file_utils.py:391 Check if a9b948e3-a2c0-4044-b131-9072f679a0d0/p2g.top exists\nINFO     /tmp/biobb/unitests_167/pmxgentop/pmxgentop_log.out:file_utils.py:391 Copying 9d760abe-e3ee-44e4-8f35-4061dbb9985d/p2g.top to: a9b948e3-a2c0-4044-b131-9072f679a0d0\nINFO     /tmp/biobb/unitests_167/pmxgentop/pmxgentop_log.out:file_utils.py:391 Check if a9b948e3-a2c0-4044-b131-9072f679a0d0/posre_Protein_chain_A.itp exists\nINFO     /tmp/biobb/unitests_167/pmxgentop/pmxgentop_log.out:file_utils.py:391 Copying 9d760abe-e3ee-44e4-8f35-4061dbb9985d/posre_Protein_chain_A.itp to: a9b948e3-a2c0-4044-b131-9072f679a0d0\nINFO     /tmp/biobb/unitests_167/pmxgentop/pmxgentop_log.out:file_utils.py:391 Check if a9b948e3-a2c0-4044-b131-9072f679a0d0/posre_Ion.itp exists\nINFO     /tmp/biobb/unitests_167/pmxgentop/pmxgentop_log.out:file_utils.py:391 Copying 9d760abe-e3ee-44e4-8f35-4061dbb9985d/posre_Ion.itp to: a9b948e3-a2c0-4044-b131-9072f679a0d0\nINFO     /tmp/biobb/unitests_167/pmxgentop/pmxgentop_log.out:file_utils.py:391 Compressing topology to: /tmp/biobb/unitests_167/pmxgentop/output_topology.zip\nINFO     /tmp/biobb/unitests_167/pmxgentop/pmxgentop_log.out:file_utils.py:203 Ignored file a9b948e3-a2c0-4044-b131-9072f679a0d0/amber99sb-star-ildn-mut.ff/forcefield.itp\nINFO     /tmp/biobb/unitests_167/pmxgentop/pmxgentop_log.out:file_utils.py:203 Ignored file a9b948e3-a2c0-4044-b131-9072f679a0d0/amber99sb-star-ildn-mut.ff/spce.itp\nINFO     /tmp/biobb/unitests_167/pmxgentop/pmxgentop_log.out:file_utils.py:203 Ignored file a9b948e3-a2c0-4044-b131-9072f679a0d0/amber99sb-star-ildn-mut.ff/ions.itp\nINFO     /tmp/biobb/unitests_167/pmxgentop/pmxgentop_log.out:file_utils.py:148 Adding:\nINFO     /tmp/biobb/unitests_167/pmxgentop/pmxgentop_log.out:file_utils.py:149 [&amp;#x27;a9b948e3-a2c0-4044-b131-9072f679a0d0/pmx_p2g_Ion.itp&amp;#x27;, &amp;#x27;a9b948e3-a2c0-4044-b131-9072f679a0d0/pmx_p2g_Protein_chain_A.itp&amp;#x27;, &amp;#x27;a9b948e3-a2c0-4044-b131-9072f679a0d0/pmxgentop_p2g.top&amp;#x27;, &amp;#x27;a9b948e3-a2c0-4044-b131-9072f679a0d0/posre_Ion.itp&amp;#x27;, &amp;#x27;a9b948e3-a2c0-4044-b131-9072f679a0d0/posre_Protein_chain_A.itp&amp;#x27;]\nINFO     /tmp/biobb/unitests_167/pmxgentop/pmxgentop_log.out:file_utils.py:150 to: /tmp/biobb/unitests_167/pmxgentop/output_topology.zip\nINFO     /tmp/biobb/unitests_167/pmxgentop/pmxgentop_log.out:file_utils.py:391 Removed: [&amp;#x27;a9b948e3-a2c0-4044-b131-9072f679a0d0/posre_Protein_chain_A.itp&amp;#x27;, &amp;#x27;a9b948e3-a2c0-4044-b131-9072f679a0d0/pmx_p2g_Protein_chain_A.itp&amp;#x27;, &amp;#x27;a9b948e3-a2c0-4044-b131-9072f679a0d0/posre_Ion.itp&amp;#x27;, &amp;#x27;a9b948e3-a2c0-4044-b131-9072f679a0d0/pmx_p2g_Ion.itp&amp;#x27;, &amp;#x27;a9b948e3-a2c0-4044-b131-9072f679a0d0/pmxgentop_p2g.top&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_167\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 -----------------------------\n2024-06-14 18:47:19,134 [MainThread  ] [INFO ]  Executing biobb_pmx.pmxbiobb.pmxligand_hybrid Version: 4.2.1\n2024-06-14 18:47:19,135 [MainThread  ] [INFO ]  /tmp/biobb/unitests_167/pmxligand_hybrid/sandbox_7b653ecb-e0d7-4170-aaaf-0a32f7c57254 directory successfully created\n2024-06-14 18:47:19,135 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/lig1.pdb to /tmp/biobb/unitests_167/pmxligand_hybrid/sandbox_7b653ecb-e0d7-4170-aaaf-0a32f7c57254\n2024-06-14 18:47:19,135 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/lig2.pdb to /tmp/biobb/unitests_167/pmxligand_hybrid/sandbox_7b653ecb-e0d7-4170-aaaf-0a32f7c57254\n2024-06-14 18:47:19,135 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/topoLig1.itp to /tmp/biobb/unitests_167/pmxligand_hybrid/sandbox_7b653ecb-e0d7-4170-aaaf-0a32f7c57254\n2024-06-14 18:47:19,136 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/topoLig2.itp to /tmp/biobb/unitests_167/pmxligand_hybrid/sandbox_7b653ecb-e0d7-4170-aaaf-0a32f7c57254\n2024-06-14 18:47:19,136 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/myPairs1.dat to /tmp/biobb/unitests_167/pmxligand_hybrid/sandbox_7b653ecb-e0d7-4170-aaaf-0a32f7c57254\n2024-06-14 18:47:19,136 [MainThread  ] [INFO ]  pmx ligandHybrid -i1 /tmp/biobb/unitests_167/pmxligand_hybrid/sandbox_7b653ecb-e0d7-4170-aaaf-0a32f7c57254/lig1.pdb -i2 /tmp/biobb/unitests_167/pmxligand_hybrid/sandbox_7b653ecb-e0d7-4170-aaaf-0a32f7c57254/lig2.pdb -itp1 /tmp/biobb/unitests_167/pmxligand_hybrid/sandbox_7b653ecb-e0d7-4170-aaaf-0a32f7c57254/topoLig1.itp -itp2 /tmp/biobb/unitests_167/pmxligand_hybrid/sandbox_7b653ecb-e0d7-4170-aaaf-0a32f7c57254/topoLig2.itp -pairs /tmp/biobb/unitests_167/pmxligand_hybrid/sandbox_7b653ecb-e0d7-4170-aaaf-0a32f7c57254/myPairs1.dat -oA /tmp/biobb/unitests_167/pmxligand_hybrid/sandbox_7b653ecb-e0d7-4170-aaaf-0a32f7c57254/hybridStruct1.pdb -oB /tmp/biobb/unitests_167/pmxligand_hybrid/sandbox_7b653ecb-e0d7-4170-aaaf-0a32f7c57254/hybridStruct2.pdb -oitp /tmp/biobb/unitests_167/pmxligand_hybrid/sandbox_7b653ecb-e0d7-4170-aaaf-0a32f7c57254/hybridTopo.itp -offitp /tmp/biobb/unitests_167/pmxligand_hybrid/sandbox_7b653ecb-e0d7-4170-aaaf-0a32f7c57254/hybridAtomTypes.itp -log /tmp/biobb/unitests_167/pmxligand_hybrid/sandbox_7b653ecb-e0d7-4170-aaaf-0a32f7c57254/ligand_hybrid.log --fit --d 0.05\n\n2024-06-14 18:47:20,748 [MainThread  ] [INFO ]  Exit code 0\n\n2024-06-14 18:47:20,749 [MainThread  ] [INFO ]  ligandHybridTop__log_&amp;gt; Reading ligand 1 from: &amp;quot;/tmp/biobb/unitests_167/pmxligand_hybrid/sandbox_7b653ecb-e0d7-4170-aaaf-0a32f7c57254/lig1.pdb&amp;quot;\nligandHybridTop__log_&amp;gt; Reading ligand 2 from: &amp;quot;/tmp/biobb/unitests_167/pmxligand_hybrid/sandbox_7b653ecb-e0d7-4170-aaaf-0a32f7c57254/lig2.pdb&amp;quot;\nligandHybridTop__log_&amp;gt; Reading topology 1 from: &amp;quot;/tmp/biobb/unitests_167/pmxligand_hybrid/sandbox_7b653ecb-e0d7-4170-aaaf-0a32f7c57254/topoLig1.itp&amp;quot;\nligandHybridTop__log_&amp;gt; Reading topology 2 from: &amp;quot;/tmp/biobb/unitests_167/pmxligand_hybrid/sandbox_7b653ecb-e0d7-4170-aaaf-0a32f7c57254/topoLig2.itp&amp;quot;\nligandHybridTop__log_&amp;gt; Reading file with atom pairs: &amp;quot;/tmp/biobb/unitests_167/pmxligand_hybrid/sandbox_7b653ecb-e0d7-4170-aaaf-0a32f7c57254/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_167/pmxligand_hybrid/sandbox_7b653ecb-e0d7-4170-aaaf-0a32f7c57254/hybridTopo.itp&amp;quot;\nligandHybridTop__log_&amp;gt; Writing dummy forcefield file: &amp;quot;/tmp/biobb/unitests_167/pmxligand_hybrid/sandbox_7b653ecb-e0d7-4170-aaaf-0a32f7c57254/hybridAtomTypes.itp&amp;quot;\n\n2024-06-14 18:47:20,750 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_167/pmxligand_hybrid/sandbox_7b653ecb-e0d7-4170-aaaf-0a32f7c57254&amp;#x27;]\nChecking if empty file: /tmp/biobb/unitests_167/pmxligand_hybrid/hybridStruct1.pdb\nChecking if empty file: /tmp/biobb/unitests_167/pmxligand_hybrid/hybridStruct2.pdb\nChecking if empty file: /tmp/biobb/unitests_167/pmxligand_hybrid/hybridTopo.itp\nChecking if empty file: /tmp/biobb/unitests_167/pmxligand_hybrid/hybridAtomTypes.itp\nChecking RMSD between:\n     PDB_A: /tmp/biobb/unitests_167/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_167/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_167/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_167/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_167/pmxligand_hybrid/pmxligand_hybrid_log.out:file_utils.py:391 Executing biobb_pmx.pmxbiobb.pmxligand_hybrid Version: 4.2.1\nINFO     /tmp/biobb/unitests_167/pmxligand_hybrid/pmxligand_hybrid_log.out:file_utils.py:82 /tmp/biobb/unitests_167/pmxligand_hybrid/sandbox_7b653ecb-e0d7-4170-aaaf-0a32f7c57254 directory successfully created\nINFO     /tmp/biobb/unitests_167/pmxligand_hybrid/pmxligand_hybrid_log.out:file_utils.py:391 Copy: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/lig1.pdb to /tmp/biobb/unitests_167/pmxligand_hybrid/sandbox_7b653ecb-e0d7-4170-aaaf-0a32f7c57254\nINFO     /tmp/biobb/unitests_167/pmxligand_hybrid/pmxligand_hybrid_log.out:file_utils.py:391 Copy: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/lig2.pdb to /tmp/biobb/unitests_167/pmxligand_hybrid/sandbox_7b653ecb-e0d7-4170-aaaf-0a32f7c57254\nINFO     /tmp/biobb/unitests_167/pmxligand_hybrid/pmxligand_hybrid_log.out:file_utils.py:391 Copy: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/topoLig1.itp to /tmp/biobb/unitests_167/pmxligand_hybrid/sandbox_7b653ecb-e0d7-4170-aaaf-0a32f7c57254\nINFO     /tmp/biobb/unitests_167/pmxligand_hybrid/pmxligand_hybrid_log.out:file_utils.py:391 Copy: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/topoLig2.itp to /tmp/biobb/unitests_167/pmxligand_hybrid/sandbox_7b653ecb-e0d7-4170-aaaf-0a32f7c57254\nINFO     /tmp/biobb/unitests_167/pmxligand_hybrid/pmxligand_hybrid_log.out:file_utils.py:391 Copy: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/myPairs1.dat to /tmp/biobb/unitests_167/pmxligand_hybrid/sandbox_7b653ecb-e0d7-4170-aaaf-0a32f7c57254\nINFO     /tmp/biobb/unitests_167/pmxligand_hybrid/pmxligand_hybrid_log.out:cmd_wrapper.py:33 pmx ligandHybrid -i1 /tmp/biobb/unitests_167/pmxligand_hybrid/sandbox_7b653ecb-e0d7-4170-aaaf-0a32f7c57254/lig1.pdb -i2 /tmp/biobb/unitests_167/pmxligand_hybrid/sandbox_7b653ecb-e0d7-4170-aaaf-0a32f7c57254/lig2.pdb -itp1 /tmp/biobb/unitests_167/pmxligand_hybrid/sandbox_7b653ecb-e0d7-4170-aaaf-0a32f7c57254/topoLig1.itp -itp2 /tmp/biobb/unitests_167/pmxligand_hybrid/sandbox_7b653ecb-e0d7-4170-aaaf-0a32f7c57254/topoLig2.itp -pairs /tmp/biobb/unitests_167/pmxligand_hybrid/sandbox_7b653ecb-e0d7-4170-aaaf-0a32f7c57254/myPairs1.dat -oA /tmp/biobb/unitests_167/pmxligand_hybrid/sandbox_7b653ecb-e0d7-4170-aaaf-0a32f7c57254/hybridStruct1.pdb -oB /tmp/biobb/unitests_167/pmxligand_hybrid/sandbox_7b653ecb-e0d7-4170-aaaf-0a32f7c57254/hybridStruct2.pdb -oitp /tmp/biobb/unitests_167/pmxligand_hybrid/sandbox_7b653ecb-e0d7-4170-aaaf-0a32f7c57254/hybridTopo.itp -offitp /tmp/biobb/unitests_167/pmxligand_hybrid/sandbox_7b653ecb-e0d7-4170-aaaf-0a32f7c57254/hybridAtomTypes.itp -log /tmp/biobb/unitests_167/pmxligand_hybrid/sandbox_7b653ecb-e0d7-4170-aaaf-0a32f7c57254/ligand_hybrid.log --fit --d 0.05\n\nINFO     /tmp/biobb/unitests_167/pmxligand_hybrid/pmxligand_hybrid_log.out:cmd_wrapper.py:50 Exit code 0\n\nINFO     /tmp/biobb/unitests_167/pmxligand_hybrid/pmxligand_hybrid_log.out:cmd_wrapper.py:52 ligandHybridTop__log_&amp;gt; Reading ligand 1 from: &amp;quot;/tmp/biobb/unitests_167/pmxligand_hybrid/sandbox_7b653ecb-e0d7-4170-aaaf-0a32f7c57254/lig1.pdb&amp;quot;\nligandHybridTop__log_&amp;gt; Reading ligand 2 from: &amp;quot;/tmp/biobb/unitests_167/pmxligand_hybrid/sandbox_7b653ecb-e0d7-4170-aaaf-0a32f7c57254/lig2.pdb&amp;quot;\nligandHybridTop__log_&amp;gt; Reading topology 1 from: &amp;quot;/tmp/biobb/unitests_167/pmxligand_hybrid/sandbox_7b653ecb-e0d7-4170-aaaf-0a32f7c57254/topoLig1.itp&amp;quot;\nligandHybridTop__log_&amp;gt; Reading topology 2 from: &amp;quot;/tmp/biobb/unitests_167/pmxligand_hybrid/sandbox_7b653ecb-e0d7-4170-aaaf-0a32f7c57254/topoLig2.itp&amp;quot;\nligandHybridTop__log_&amp;gt; Reading file with atom pairs: &amp;quot;/tmp/biobb/unitests_167/pmxligand_hybrid/sandbox_7b653ecb-e0d7-4170-aaaf-0a32f7c57254/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_167/pmxligand_hybrid/sandbox_7b653ecb-e0d7-4170-aaaf-0a32f7c57254/hybridTopo.itp&amp;quot;\nligandHybridTop__log_&amp;gt; Writing dummy forcefield file: &amp;quot;/tmp/biobb/unitests_167/pmxligand_hybrid/sandbox_7b653ecb-e0d7-4170-aaaf-0a32f7c57254/hybridAtomTypes.itp&amp;quot;\n\nINFO     /tmp/biobb/unitests_167/pmxligand_hybrid/pmxligand_hybrid_log.out:file_utils.py:391 Removed: [&amp;#x27;/tmp/biobb/unitests_167/pmxligand_hybrid/sandbox_7b653ecb-e0d7-4170-aaaf-0a32f7c57254&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_167\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;33 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;33 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 -----------------------------\n2024-06-14 18:47:20,797 [MainThread  ] [INFO ]  Executing biobb_pmx.pmxbiobb.pmxmerge_ff Version: 4.2.1\n2024-06-14 18:47:20,797 [MainThread  ] [INFO ]  /tmp/biobb/unitests_167/pmxmerge_ff/sandbox_ea23f37f-0311-4560-8c15-2c70ee815c76 directory successfully created\n2024-06-14 18:47:20,797 [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_167/pmxmerge_ff/sandbox_ea23f37f-0311-4560-8c15-2c70ee815c76\n2024-06-14 18:47:20,797 [MainThread  ] [INFO ]  Creating c1ccff03-6d76-4727-b1e5-bce657756b2c temporary folder\n2024-06-14 18:47:20,798 [MainThread  ] [INFO ]  Extracting: /tmp/biobb/unitests_167/pmxmerge_ff/sandbox_ea23f37f-0311-4560-8c15-2c70ee815c76/itps_to_merge.zip\n2024-06-14 18:47:20,798 [MainThread  ] [INFO ]  to:\n2024-06-14 18:47:20,798 [MainThread  ] [INFO ]  [&amp;#x27;c1ccff03-6d76-4727-b1e5-bce657756b2c/myHybridAtomTypes.itp&amp;#x27;, &amp;#x27;c1ccff03-6d76-4727-b1e5-bce657756b2c/lig1ffMOL.itp&amp;#x27;, &amp;#x27;c1ccff03-6d76-4727-b1e5-bce657756b2c/lig2ffMOL.itp&amp;#x27;]\n2024-06-14 18:47:20,799 [MainThread  ] [INFO ]  Running merge_FF_files from pmx package...\n\n2024-06-14 18:47:20,799 [MainThread  ] [INFO ]  Exit code 0\n\n2024-06-14 18:47:20,799 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_167/pmxmerge_ff/sandbox_ea23f37f-0311-4560-8c15-2c70ee815c76&amp;#x27;]\nChecking if empty file: /tmp/biobb/unitests_167/pmxmerge_ff/hybridTopo.itp\nComparing size of both files:\n     FILE_A: /tmp/biobb/unitests_167/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_167/pmxmerge_ff/pmxmerge_ff_log.out:file_utils.py:391 Executing biobb_pmx.pmxbiobb.pmxmerge_ff Version: 4.2.1\nINFO     /tmp/biobb/unitests_167/pmxmerge_ff/pmxmerge_ff_log.out:file_utils.py:82 /tmp/biobb/unitests_167/pmxmerge_ff/sandbox_ea23f37f-0311-4560-8c15-2c70ee815c76 directory successfully created\nINFO     /tmp/biobb/unitests_167/pmxmerge_ff/pmxmerge_ff_log.out:file_utils.py:391 Copy: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/itps_to_merge.zip to /tmp/biobb/unitests_167/pmxmerge_ff/sandbox_ea23f37f-0311-4560-8c15-2c70ee815c76\nINFO     /tmp/biobb/unitests_167/pmxmerge_ff/pmxmerge_ff_log.out:file_utils.py:391 Creating c1ccff03-6d76-4727-b1e5-bce657756b2c temporary folder\nINFO     /tmp/biobb/unitests_167/pmxmerge_ff/pmxmerge_ff_log.out:file_utils.py:172 Extracting: /tmp/biobb/unitests_167/pmxmerge_ff/sandbox_ea23f37f-0311-4560-8c15-2c70ee815c76/itps_to_merge.zip\nINFO     /tmp/biobb/unitests_167/pmxmerge_ff/pmxmerge_ff_log.out:file_utils.py:173 to:\nINFO     /tmp/biobb/unitests_167/pmxmerge_ff/pmxmerge_ff_log.out:file_utils.py:174 [&amp;#x27;c1ccff03-6d76-4727-b1e5-bce657756b2c/myHybridAtomTypes.itp&amp;#x27;, &amp;#x27;c1ccff03-6d76-4727-b1e5-bce657756b2c/lig1ffMOL.itp&amp;#x27;, &amp;#x27;c1ccff03-6d76-4727-b1e5-bce657756b2c/lig2ffMOL.itp&amp;#x27;]\nINFO     /tmp/biobb/unitests_167/pmxmerge_ff/pmxmerge_ff_log.out:file_utils.py:391 Running merge_FF_files from pmx package...\n\nINFO     /tmp/biobb/unitests_167/pmxmerge_ff/pmxmerge_ff_log.out:file_utils.py:391 Exit code 0\n\nINFO     /tmp/biobb/unitests_167/pmxmerge_ff/pmxmerge_ff_log.out:file_utils.py:391 Removed: [&amp;#x27;/tmp/biobb/unitests_167/pmxmerge_ff/sandbox_ea23f37f-0311-4560-8c15-2c70ee815c76&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_167\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 -----------------------------\n2024-06-14 18:47:20,830 [MainThread  ] [INFO ]  Executing biobb_pmx.pmxbiobb.pmxmutate Version: 4.2.1\n2024-06-14 18:47:20,830 [MainThread  ] [INFO ]  /tmp/biobb/unitests_167/pmxmutate/sandbox_e1d06b5d-2b4a-4b4a-a1d5-ce64d481b330 directory successfully created\n2024-06-14 18:47:20,833 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/frameA0.pdb to /tmp/biobb/unitests_167/pmxmutate/sandbox_e1d06b5d-2b4a-4b4a-a1d5-ce64d481b330\n2024-06-14 18:47:20,834 [MainThread  ] [INFO ]  pmx mutate -f /tmp/biobb/unitests_167/pmxmutate/sandbox_e1d06b5d-2b4a-4b4a-a1d5-ce64d481b330/frameA0.pdb -o /tmp/biobb/unitests_167/pmxmutate/sandbox_e1d06b5d-2b4a-4b4a-a1d5-ce64d481b330/output_structure.pdb -ff amber99sb-star-ildn-mut --script a065e671-5df5-432d-8bca-16c50776298f/mutations.txt\n\n2024-06-14 18:47:23,643 [MainThread  ] [INFO ]  Exit code 0\n\n2024-06-14 18:47:23,644 [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\n2024-06-14 18:47:23,647 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_167/pmxmutate/sandbox_e1d06b5d-2b4a-4b4a-a1d5-ce64d481b330&amp;#x27;]\nChecking if empty file: /tmp/biobb/unitests_167/pmxmutate/output_structure.pdb\nChecking RMSD between:\n     PDB_A: /tmp/biobb/unitests_167/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_167/pmxmutate/pmxmutate_log.out:file_utils.py:391 Executing biobb_pmx.pmxbiobb.pmxmutate Version: 4.2.1\nINFO     /tmp/biobb/unitests_167/pmxmutate/pmxmutate_log.out:file_utils.py:82 /tmp/biobb/unitests_167/pmxmutate/sandbox_e1d06b5d-2b4a-4b4a-a1d5-ce64d481b330 directory successfully created\nINFO     /tmp/biobb/unitests_167/pmxmutate/pmxmutate_log.out:file_utils.py:391 Copy: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/frameA0.pdb to /tmp/biobb/unitests_167/pmxmutate/sandbox_e1d06b5d-2b4a-4b4a-a1d5-ce64d481b330\nINFO     /tmp/biobb/unitests_167/pmxmutate/pmxmutate_log.out:cmd_wrapper.py:33 pmx mutate -f /tmp/biobb/unitests_167/pmxmutate/sandbox_e1d06b5d-2b4a-4b4a-a1d5-ce64d481b330/frameA0.pdb -o /tmp/biobb/unitests_167/pmxmutate/sandbox_e1d06b5d-2b4a-4b4a-a1d5-ce64d481b330/output_structure.pdb -ff amber99sb-star-ildn-mut --script a065e671-5df5-432d-8bca-16c50776298f/mutations.txt\n\nINFO     /tmp/biobb/unitests_167/pmxmutate/pmxmutate_log.out:cmd_wrapper.py:50 Exit code 0\n\nINFO     /tmp/biobb/unitests_167/pmxmutate/pmxmutate_log.out:cmd_wrapper.py:52 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_167/pmxmutate/pmxmutate_log.out:file_utils.py:391 Removed: [&amp;#x27;/tmp/biobb/unitests_167/pmxmutate/sandbox_e1d06b5d-2b4a-4b4a-a1d5-ce64d481b330&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_167\n&#34;}]}, &#34;renderCollapsed&#34;: [&#34;passed&#34;], &#34;initialSort&#34;: &#34;result&#34;, &#34;title&#34;: &#34;report.html&#34;}"></div>
+    <div id="data-container" data-jsonblob="{&#34;environment&#34;: {&#34;Python&#34;: &#34;3.10.14&#34;, &#34;Platform&#34;: &#34;Linux-5.4.0-159-generic-x86_64-with-glibc2.31&#34;, &#34;Packages&#34;: {&#34;pytest&#34;: &#34;8.2.2&#34;, &#34;pluggy&#34;: &#34;1.5.0&#34;}, &#34;Plugins&#34;: {&#34;metadata&#34;: &#34;3.1.1&#34;, &#34;html&#34;: &#34;4.1.1&#34;, &#34;cov&#34;: &#34;5.0.0&#34;}, &#34;CI&#34;: &#34;true&#34;}, &#34;tests&#34;: {&#34;biobb_pmx/test/unitests/test_pmx/test_pmxanalyse.py::TestPmxanalyse::test_pmxanalyse&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_pmx/test/unitests/test_pmx/test_pmxanalyse.py::TestPmxanalyse::test_pmxanalyse&#34;, &#34;duration&#34;: &#34;00:00:13&#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_pmxanalyse.py::TestPmxanalyse::test_pmxanalyse&lt;/td&gt;&#34;, &#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 -----------------------------\n2024-06-14 18:54:09,992 [MainThread  ] [INFO ]  Executing biobb_pmx.pmxbiobb.pmxanalyse Version: 4.2.1\n2024-06-14 18:54:09,992 [MainThread  ] [INFO ]  /tmp/biobb/unitests_167/pmxanalyse/sandbox_d5a33a94-c627-4f23-ac7c-6c775f29a832 directory successfully created\n2024-06-14 18:54:10,271 [MainThread  ] [INFO ]  Extracting: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/xvg_A.zip\n2024-06-14 18:54:10,271 [MainThread  ] [INFO ]  to:\n2024-06-14 18:54:10,271 [MainThread  ] [INFO ]  [&amp;#x27;851c5317-7a22-4489-9f12-93a8bf8e40d0/frame0/dhdl0.xvg&amp;#x27;, &amp;#x27;851c5317-7a22-4489-9f12-93a8bf8e40d0/frame1/dhdl1.xvg&amp;#x27;, &amp;#x27;851c5317-7a22-4489-9f12-93a8bf8e40d0/frame10/dhdl10.xvg&amp;#x27;, 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&amp;#x27;851c5317-7a22-4489-9f12-93a8bf8e40d0/frame94/dhdl94.xvg&amp;#x27;, &amp;#x27;851c5317-7a22-4489-9f12-93a8bf8e40d0/frame95/dhdl95.xvg&amp;#x27;, &amp;#x27;851c5317-7a22-4489-9f12-93a8bf8e40d0/frame96/dhdl96.xvg&amp;#x27;, &amp;#x27;851c5317-7a22-4489-9f12-93a8bf8e40d0/frame97/dhdl97.xvg&amp;#x27;, &amp;#x27;851c5317-7a22-4489-9f12-93a8bf8e40d0/frame98/dhdl98.xvg&amp;#x27;, &amp;#x27;851c5317-7a22-4489-9f12-93a8bf8e40d0/frame99/dhdl99.xvg&amp;#x27;]\n2024-06-14 18:54:10,557 [MainThread  ] [INFO ]  Extracting: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/xvg_B.zip\n2024-06-14 18:54:10,557 [MainThread  ] [INFO ]  to:\n2024-06-14 18:54:10,557 [MainThread  ] [INFO ]  [&amp;#x27;fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame0/dhdl0.xvg&amp;#x27;, &amp;#x27;fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame1/dhdl1.xvg&amp;#x27;, &amp;#x27;fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame10/dhdl10.xvg&amp;#x27;, 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&amp;#x27;fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame94/dhdl94.xvg&amp;#x27;, &amp;#x27;fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame95/dhdl95.xvg&amp;#x27;, &amp;#x27;fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame96/dhdl96.xvg&amp;#x27;, &amp;#x27;fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame97/dhdl97.xvg&amp;#x27;, &amp;#x27;fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame98/dhdl98.xvg&amp;#x27;, &amp;#x27;fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame99/dhdl99.xvg&amp;#x27;]\n2024-06-14 18:54:10,560 [MainThread  ] [INFO ]  pmx analyse -fA 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame0/dhdl0.xvg 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame1/dhdl1.xvg 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame10/dhdl10.xvg 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame11/dhdl11.xvg 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame12/dhdl12.xvg 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame13/dhdl13.xvg 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame14/dhdl14.xvg 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame15/dhdl15.xvg 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame16/dhdl16.xvg 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame17/dhdl17.xvg 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame18/dhdl18.xvg 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame19/dhdl19.xvg 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame2/dhdl2.xvg 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame20/dhdl20.xvg 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame21/dhdl21.xvg 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame22/dhdl22.xvg 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame23/dhdl23.xvg 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame24/dhdl24.xvg 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame25/dhdl25.xvg 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame26/dhdl26.xvg 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame27/dhdl27.xvg 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame28/dhdl28.xvg 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame29/dhdl29.xvg 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame3/dhdl3.xvg 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame30/dhdl30.xvg 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame31/dhdl31.xvg 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame32/dhdl32.xvg 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame33/dhdl33.xvg 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame34/dhdl34.xvg 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame35/dhdl35.xvg 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame36/dhdl36.xvg 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame37/dhdl37.xvg 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame38/dhdl38.xvg 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame39/dhdl39.xvg 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame4/dhdl4.xvg 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame40/dhdl40.xvg 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame41/dhdl41.xvg 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame42/dhdl42.xvg 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame43/dhdl43.xvg 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame44/dhdl44.xvg 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame45/dhdl45.xvg 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame46/dhdl46.xvg 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame47/dhdl47.xvg 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame48/dhdl48.xvg 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame49/dhdl49.xvg 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame5/dhdl5.xvg 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame50/dhdl50.xvg 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame51/dhdl51.xvg 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame52/dhdl52.xvg 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame53/dhdl53.xvg 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame54/dhdl54.xvg 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame55/dhdl55.xvg 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame56/dhdl56.xvg 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame57/dhdl57.xvg 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame58/dhdl58.xvg 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame59/dhdl59.xvg 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame6/dhdl6.xvg 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame60/dhdl60.xvg 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame61/dhdl61.xvg 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame62/dhdl62.xvg 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame63/dhdl63.xvg 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame64/dhdl64.xvg 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame65/dhdl65.xvg 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame66/dhdl66.xvg 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame67/dhdl67.xvg 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame68/dhdl68.xvg 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame69/dhdl69.xvg 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame7/dhdl7.xvg 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame70/dhdl70.xvg 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame71/dhdl71.xvg 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame72/dhdl72.xvg 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame73/dhdl73.xvg 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame74/dhdl74.xvg 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame75/dhdl75.xvg 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame76/dhdl76.xvg 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame77/dhdl77.xvg 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame78/dhdl78.xvg 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame79/dhdl79.xvg 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame8/dhdl8.xvg 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame80/dhdl80.xvg 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame81/dhdl81.xvg 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame82/dhdl82.xvg 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame83/dhdl83.xvg 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame84/dhdl84.xvg 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame85/dhdl85.xvg 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame86/dhdl86.xvg 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame87/dhdl87.xvg 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame88/dhdl88.xvg 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame89/dhdl89.xvg 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame9/dhdl9.xvg 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame90/dhdl90.xvg 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame91/dhdl91.xvg 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame92/dhdl92.xvg 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame93/dhdl93.xvg 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame94/dhdl94.xvg 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame95/dhdl95.xvg 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame96/dhdl96.xvg 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame97/dhdl97.xvg 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame98/dhdl98.xvg 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame99/dhdl99.xvg -fB fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame0/dhdl0.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame1/dhdl1.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame10/dhdl10.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame11/dhdl11.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame12/dhdl12.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame13/dhdl13.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame14/dhdl14.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame15/dhdl15.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame16/dhdl16.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame17/dhdl17.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame18/dhdl18.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame19/dhdl19.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame2/dhdl2.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame20/dhdl20.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame21/dhdl21.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame22/dhdl22.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame23/dhdl23.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame24/dhdl24.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame25/dhdl25.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame26/dhdl26.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame27/dhdl27.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame28/dhdl28.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame29/dhdl29.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame3/dhdl3.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame30/dhdl30.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame31/dhdl31.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame32/dhdl32.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame33/dhdl33.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame34/dhdl34.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame35/dhdl35.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame36/dhdl36.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame37/dhdl37.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame38/dhdl38.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame39/dhdl39.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame4/dhdl4.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame40/dhdl40.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame41/dhdl41.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame42/dhdl42.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame43/dhdl43.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame44/dhdl44.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame45/dhdl45.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame46/dhdl46.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame47/dhdl47.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame48/dhdl48.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame49/dhdl49.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame5/dhdl5.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame50/dhdl50.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame51/dhdl51.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame52/dhdl52.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame53/dhdl53.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame54/dhdl54.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame55/dhdl55.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame56/dhdl56.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame57/dhdl57.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame58/dhdl58.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame59/dhdl59.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame6/dhdl6.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame60/dhdl60.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame61/dhdl61.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame62/dhdl62.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame63/dhdl63.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame64/dhdl64.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame65/dhdl65.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame66/dhdl66.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame67/dhdl67.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame68/dhdl68.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame69/dhdl69.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame7/dhdl7.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame70/dhdl70.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame71/dhdl71.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame72/dhdl72.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame73/dhdl73.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame74/dhdl74.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame75/dhdl75.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame76/dhdl76.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame77/dhdl77.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame78/dhdl78.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame79/dhdl79.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame8/dhdl8.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame80/dhdl80.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame81/dhdl81.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame82/dhdl82.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame83/dhdl83.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame84/dhdl84.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame85/dhdl85.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame86/dhdl86.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame87/dhdl87.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame88/dhdl88.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame89/dhdl89.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame9/dhdl9.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame90/dhdl90.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame91/dhdl91.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame92/dhdl92.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame93/dhdl93.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame94/dhdl94.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame95/dhdl95.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame96/dhdl96.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame97/dhdl97.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame98/dhdl98.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame99/dhdl99.xvg -o /tmp/biobb/unitests_167/pmxanalyse/sandbox_d5a33a94-c627-4f23-ac7c-6c775f29a832/result.txt -w /tmp/biobb/unitests_167/pmxanalyse/sandbox_d5a33a94-c627-4f23-ac7c-6c775f29a832/plot.png -m CGI BAR JARZ -t 298.15 -n 1 --skip 1 --prec 2 --units kJ --nbins 20 --dpi 600\n\n2024-06-14 18:54:21,993 [MainThread  ] [INFO ]  Exit code 0\n\n2024-06-14 18:54:21,993 [MainThread  ] [INFO ]  \n\n ========================================================\n                   PROCESSING THE DATA\n ========================================================\n  Forward Data\n    First accepted file: 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame0/dhdl0.xvg\n    # data points: 25001\n    Length of trajectory:   50.000 ps\n    Delta lambda:  0.00004\n\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame1/dhdl1.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame2/dhdl2.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame3/dhdl3.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame4/dhdl4.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame5/dhdl5.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame6/dhdl6.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame7/dhdl7.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame8/dhdl8.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame9/dhdl9.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame10/dhdl10.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame11/dhdl11.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame12/dhdl12.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame13/dhdl13.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame14/dhdl14.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame15/dhdl15.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame16/dhdl16.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame17/dhdl17.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame18/dhdl18.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame19/dhdl19.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame20/dhdl20.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame21/dhdl21.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame22/dhdl22.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame23/dhdl23.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame24/dhdl24.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame25/dhdl25.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame26/dhdl26.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame27/dhdl27.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame28/dhdl28.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame29/dhdl29.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame30/dhdl30.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame31/dhdl31.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame32/dhdl32.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame33/dhdl33.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame34/dhdl34.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame35/dhdl35.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame36/dhdl36.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame37/dhdl37.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame38/dhdl38.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame39/dhdl39.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame40/dhdl40.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame41/dhdl41.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame42/dhdl42.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame43/dhdl43.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame44/dhdl44.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame45/dhdl45.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame46/dhdl46.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame47/dhdl47.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame48/dhdl48.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame49/dhdl49.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame50/dhdl50.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame51/dhdl51.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame52/dhdl52.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame53/dhdl53.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame54/dhdl54.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame55/dhdl55.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame56/dhdl56.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame57/dhdl57.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame58/dhdl58.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame59/dhdl59.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame60/dhdl60.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame61/dhdl61.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame62/dhdl62.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame63/dhdl63.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame64/dhdl64.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame65/dhdl65.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame66/dhdl66.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame67/dhdl67.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame68/dhdl68.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame69/dhdl69.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame70/dhdl70.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame71/dhdl71.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame72/dhdl72.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame73/dhdl73.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame74/dhdl74.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame75/dhdl75.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame76/dhdl76.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame77/dhdl77.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame78/dhdl78.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame79/dhdl79.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame80/dhdl80.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame81/dhdl81.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame82/dhdl82.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame83/dhdl83.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame84/dhdl84.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame85/dhdl85.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame86/dhdl86.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame87/dhdl87.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame88/dhdl88.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame89/dhdl89.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame90/dhdl90.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame91/dhdl91.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame92/dhdl92.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame93/dhdl93.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame94/dhdl94.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame95/dhdl95.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame96/dhdl96.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame97/dhdl97.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame98/dhdl98.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame99/dhdl99.xvg\n\n  Reverse Data\n    First accepted file: fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame0/dhdl0.xvg\n    # data points: 25001\n    Length of trajectory:   50.000 ps\n    Delta lambda: -0.00004\n\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame1/dhdl1.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame2/dhdl2.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame3/dhdl3.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame4/dhdl4.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame5/dhdl5.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame6/dhdl6.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame7/dhdl7.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame8/dhdl8.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame9/dhdl9.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame10/dhdl10.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame11/dhdl11.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame12/dhdl12.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame13/dhdl13.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame14/dhdl14.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame15/dhdl15.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame16/dhdl16.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame17/dhdl17.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame18/dhdl18.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame19/dhdl19.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame20/dhdl20.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame21/dhdl21.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame22/dhdl22.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame23/dhdl23.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame24/dhdl24.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame25/dhdl25.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame26/dhdl26.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame27/dhdl27.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame28/dhdl28.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame29/dhdl29.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame30/dhdl30.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame31/dhdl31.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame32/dhdl32.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame33/dhdl33.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame34/dhdl34.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame35/dhdl35.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame36/dhdl36.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame37/dhdl37.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame38/dhdl38.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame39/dhdl39.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame40/dhdl40.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame41/dhdl41.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame42/dhdl42.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame43/dhdl43.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame44/dhdl44.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame45/dhdl45.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame46/dhdl46.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame47/dhdl47.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame48/dhdl48.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame49/dhdl49.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame50/dhdl50.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame51/dhdl51.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame52/dhdl52.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame53/dhdl53.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame54/dhdl54.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame55/dhdl55.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame56/dhdl56.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame57/dhdl57.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame58/dhdl58.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame59/dhdl59.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame60/dhdl60.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame61/dhdl61.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame62/dhdl62.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame63/dhdl63.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame64/dhdl64.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame65/dhdl65.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame66/dhdl66.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame67/dhdl67.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame68/dhdl68.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame69/dhdl69.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame70/dhdl70.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame71/dhdl71.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame72/dhdl72.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame73/dhdl73.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame74/dhdl74.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame75/dhdl75.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame76/dhdl76.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame77/dhdl77.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame78/dhdl78.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame79/dhdl79.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame80/dhdl80.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame81/dhdl81.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame82/dhdl82.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame83/dhdl83.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame84/dhdl84.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame85/dhdl85.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame86/dhdl86.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame87/dhdl87.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame88/dhdl88.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame89/dhdl89.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame90/dhdl90.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame91/dhdl91.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame92/dhdl92.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame93/dhdl93.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame94/dhdl94.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame95/dhdl95.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame96/dhdl96.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame97/dhdl97.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame98/dhdl98.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/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  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dG =     8.39 kJ/mol\n  CGI: Std Err (bootstrap:parametric) =     0.43 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 9/100\r  Bootstrap (Std Err): iteration 10/100\r  Bootstrap (Std Err): iteration 11/100\r  Bootstrap (Std Err): iteration 12/100\r  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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) =     0.54 kJ/mol\n  JARZ: Std Err Reverse (bootstrap) =     2.55 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  Bootstrap (Std Err): iteration 17/100\r  Bootstrap (Std Err): iteration 18/100\r  Bootstrap (Std Err): iteration 19/100\r  Bootstrap 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41/100\r  Bootstrap (Std Err): iteration 42/100\r  Bootstrap (Std Err): iteration 43/100\r  Bootstrap (Std Err): iteration 44/100\r  Bootstrap (Std Err): iteration 45/100\r  Bootstrap (Std Err): iteration 46/100\r  Bootstrap (Std Err): iteration 47/100\r  Bootstrap (Std Err): iteration 48/100\r  Bootstrap (Std Err): iteration 49/100\r  Bootstrap (Std Err): iteration 50/100\r  Bootstrap (Std Err): iteration 51/100\r  Bootstrap (Std Err): iteration 52/100\r  Bootstrap (Std Err): iteration 53/100\r  Bootstrap (Std Err): iteration 54/100\r  Bootstrap (Std Err): iteration 55/100\r  Bootstrap (Std Err): iteration 56/100\r  Bootstrap (Std Err): iteration 57/100\r  Bootstrap (Std Err): iteration 58/100\r  Bootstrap (Std Err): iteration 59/100\r  Bootstrap (Std Err): iteration 60/100\r  Bootstrap (Std Err): iteration 61/100\r  Bootstrap (Std Err): iteration 62/100\r  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) =     0.68 kJ/mol\n  JARZ_Gauss: Std Err Reverse (bootstrap) =     2.58 kJ/mol\n ========================================================\n\n   Plotting histograms......\n\n   ......done...........\n\n   Execution time = 00:00:10\n\n\n2024-06-14 18:54:22,018 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fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame35/dhdl35.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame36/dhdl36.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame37/dhdl37.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame38/dhdl38.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame39/dhdl39.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame4/dhdl4.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame40/dhdl40.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame41/dhdl41.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame42/dhdl42.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame43/dhdl43.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame44/dhdl44.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame45/dhdl45.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame46/dhdl46.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame47/dhdl47.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame48/dhdl48.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame49/dhdl49.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame5/dhdl5.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame50/dhdl50.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame51/dhdl51.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame52/dhdl52.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame53/dhdl53.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame54/dhdl54.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame55/dhdl55.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame56/dhdl56.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame57/dhdl57.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame58/dhdl58.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame59/dhdl59.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame6/dhdl6.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame60/dhdl60.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame61/dhdl61.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame62/dhdl62.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame63/dhdl63.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame64/dhdl64.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame65/dhdl65.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame66/dhdl66.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame67/dhdl67.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame68/dhdl68.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame69/dhdl69.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame7/dhdl7.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame70/dhdl70.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame71/dhdl71.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame72/dhdl72.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame73/dhdl73.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame74/dhdl74.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame75/dhdl75.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame76/dhdl76.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame77/dhdl77.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame78/dhdl78.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame79/dhdl79.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame8/dhdl8.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame80/dhdl80.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame81/dhdl81.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame82/dhdl82.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame83/dhdl83.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame84/dhdl84.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame85/dhdl85.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame86/dhdl86.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame87/dhdl87.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame88/dhdl88.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame89/dhdl89.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame9/dhdl9.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame90/dhdl90.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame91/dhdl91.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame92/dhdl92.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame93/dhdl93.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame94/dhdl94.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame95/dhdl95.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame96/dhdl96.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame97/dhdl97.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame98/dhdl98.xvg fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame99/dhdl99.xvg -o /tmp/biobb/unitests_167/pmxanalyse/sandbox_d5a33a94-c627-4f23-ac7c-6c775f29a832/result.txt -w /tmp/biobb/unitests_167/pmxanalyse/sandbox_d5a33a94-c627-4f23-ac7c-6c775f29a832/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_167/pmxanalyse/pmxanalyse_log.out:cmd_wrapper.py:50 Exit code 0\n\nINFO     /tmp/biobb/unitests_167/pmxanalyse/pmxanalyse_log.out:cmd_wrapper.py:52 \n\n ========================================================\n                   PROCESSING THE DATA\n ========================================================\n  Forward Data\n    First accepted file: 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame0/dhdl0.xvg\n    # data points: 25001\n    Length of trajectory:   50.000 ps\n    Delta lambda:  0.00004\n\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame1/dhdl1.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame2/dhdl2.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame3/dhdl3.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame4/dhdl4.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame5/dhdl5.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame6/dhdl6.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame7/dhdl7.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame8/dhdl8.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame9/dhdl9.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame10/dhdl10.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame11/dhdl11.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame12/dhdl12.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame13/dhdl13.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame14/dhdl14.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame15/dhdl15.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame16/dhdl16.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame17/dhdl17.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame18/dhdl18.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame19/dhdl19.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame20/dhdl20.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame21/dhdl21.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame22/dhdl22.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame23/dhdl23.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame24/dhdl24.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame25/dhdl25.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame26/dhdl26.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame27/dhdl27.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame28/dhdl28.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame29/dhdl29.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame30/dhdl30.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame31/dhdl31.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame32/dhdl32.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame33/dhdl33.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame34/dhdl34.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame35/dhdl35.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame36/dhdl36.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame37/dhdl37.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame38/dhdl38.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame39/dhdl39.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame40/dhdl40.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame41/dhdl41.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame42/dhdl42.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame43/dhdl43.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame44/dhdl44.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame45/dhdl45.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame46/dhdl46.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame47/dhdl47.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame48/dhdl48.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame49/dhdl49.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame50/dhdl50.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame51/dhdl51.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame52/dhdl52.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame53/dhdl53.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame54/dhdl54.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame55/dhdl55.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame56/dhdl56.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame57/dhdl57.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame58/dhdl58.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame59/dhdl59.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame60/dhdl60.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame61/dhdl61.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame62/dhdl62.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame63/dhdl63.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame64/dhdl64.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame65/dhdl65.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame66/dhdl66.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame67/dhdl67.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame68/dhdl68.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame69/dhdl69.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame70/dhdl70.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame71/dhdl71.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame72/dhdl72.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame73/dhdl73.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame74/dhdl74.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame75/dhdl75.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame76/dhdl76.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame77/dhdl77.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame78/dhdl78.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame79/dhdl79.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame80/dhdl80.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame81/dhdl81.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame82/dhdl82.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame83/dhdl83.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame84/dhdl84.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame85/dhdl85.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame86/dhdl86.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame87/dhdl87.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame88/dhdl88.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame89/dhdl89.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame90/dhdl90.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame91/dhdl91.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame92/dhdl92.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame93/dhdl93.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame94/dhdl94.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame95/dhdl95.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame96/dhdl96.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame97/dhdl97.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame98/dhdl98.xvg\r    Reading 851c5317-7a22-4489-9f12-93a8bf8e40d0/frame99/dhdl99.xvg\n\n  Reverse Data\n    First accepted file: fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame0/dhdl0.xvg\n    # data points: 25001\n    Length of trajectory:   50.000 ps\n    Delta lambda: -0.00004\n\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame1/dhdl1.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame2/dhdl2.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame3/dhdl3.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame4/dhdl4.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame5/dhdl5.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame6/dhdl6.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame7/dhdl7.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame8/dhdl8.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame9/dhdl9.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame10/dhdl10.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame11/dhdl11.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame12/dhdl12.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame13/dhdl13.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame14/dhdl14.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame15/dhdl15.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame16/dhdl16.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame17/dhdl17.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame18/dhdl18.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame19/dhdl19.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame20/dhdl20.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame21/dhdl21.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame22/dhdl22.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame23/dhdl23.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame24/dhdl24.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame25/dhdl25.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame26/dhdl26.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame27/dhdl27.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame28/dhdl28.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame29/dhdl29.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame30/dhdl30.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame31/dhdl31.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame32/dhdl32.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame33/dhdl33.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame34/dhdl34.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame35/dhdl35.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame36/dhdl36.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame37/dhdl37.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame38/dhdl38.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame39/dhdl39.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame40/dhdl40.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame41/dhdl41.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame42/dhdl42.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame43/dhdl43.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame44/dhdl44.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame45/dhdl45.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame46/dhdl46.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame47/dhdl47.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame48/dhdl48.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame49/dhdl49.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame50/dhdl50.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame51/dhdl51.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame52/dhdl52.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame53/dhdl53.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame54/dhdl54.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame55/dhdl55.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame56/dhdl56.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame57/dhdl57.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame58/dhdl58.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame59/dhdl59.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame60/dhdl60.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame61/dhdl61.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame62/dhdl62.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame63/dhdl63.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame64/dhdl64.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame65/dhdl65.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame66/dhdl66.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame67/dhdl67.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame68/dhdl68.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame69/dhdl69.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame70/dhdl70.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame71/dhdl71.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame72/dhdl72.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame73/dhdl73.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame74/dhdl74.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame75/dhdl75.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame76/dhdl76.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame77/dhdl77.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame78/dhdl78.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame79/dhdl79.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame80/dhdl80.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame81/dhdl81.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame82/dhdl82.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame83/dhdl83.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame84/dhdl84.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame85/dhdl85.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame86/dhdl86.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame87/dhdl87.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame88/dhdl88.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame89/dhdl89.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame90/dhdl90.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame91/dhdl91.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame92/dhdl92.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame93/dhdl93.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame94/dhdl94.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame95/dhdl95.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame96/dhdl96.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame97/dhdl97.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/frame98/dhdl98.xvg\r    Reading fe85eda2-45b4-46f7-b5a7-9588f43324f4/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 20/100\r  Bootstrap (Std Err): iteration 21/100\r  Bootstrap (Std Err): iteration 22/100\r  Bootstrap (Std Err): iteration 23/100\r  Bootstrap (Std Err): iteration 24/100\r  Bootstrap (Std Err): iteration 25/100\r  Bootstrap (Std Err): iteration 26/100\r  Bootstrap (Std Err): iteration 27/100\r  Bootstrap (Std Err): iteration 28/100\r  Bootstrap (Std Err): iteration 29/100\r  Bootstrap (Std Err): iteration 30/100\r  Bootstrap (Std Err): iteration 31/100\r  Bootstrap (Std Err): iteration 32/100\r  Bootstrap (Std Err): iteration 33/100\r  Bootstrap (Std Err): iteration 34/100\r  Bootstrap (Std Err): iteration 35/100\r  Bootstrap (Std Err): iteration 36/100\r  Bootstrap (Std Err): iteration 37/100\r  Bootstrap (Std Err): iteration 38/100\r  Bootstrap (Std Err): iteration 39/100\r  Bootstrap (Std Err): iteration 40/100\r  Bootstrap (Std Err): iteration 41/100\r  Bootstrap (Std Err): iteration 42/100\r  Bootstrap (Std Err): iteration 43/100\r  Bootstrap (Std Err): iteration 44/100\r  Bootstrap (Std Err): iteration 45/100\r  Bootstrap (Std Err): iteration 46/100\r  Bootstrap (Std Err): iteration 47/100\r  Bootstrap (Std Err): iteration 48/100\r  Bootstrap (Std Err): iteration 49/100\r  Bootstrap (Std Err): iteration 50/100\r  Bootstrap (Std Err): iteration 51/100\r  Bootstrap (Std Err): iteration 52/100\r  Bootstrap (Std Err): iteration 53/100\r  Bootstrap (Std Err): iteration 54/100\r  Bootstrap (Std Err): iteration 55/100\r  Bootstrap (Std Err): iteration 56/100\r  Bootstrap (Std Err): iteration 57/100\r  Bootstrap (Std Err): iteration 58/100\r  Bootstrap (Std Err): iteration 59/100\r  Bootstrap (Std Err): iteration 60/100\r  Bootstrap (Std Err): iteration 61/100\r  Bootstrap (Std Err): iteration 62/100\r  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  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) =     0.43 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 9/100\r  Bootstrap (Std Err): iteration 10/100\r  Bootstrap (Std Err): iteration 11/100\r  Bootstrap (Std Err): iteration 12/100\r  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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) =     0.54 kJ/mol\n  JARZ: Std Err Reverse (bootstrap) =     2.55 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  Bootstrap (Std Err): iteration 17/100\r  Bootstrap (Std Err): iteration 18/100\r  Bootstrap (Std Err): iteration 19/100\r  Bootstrap 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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) =     0.68 kJ/mol\n  JARZ_Gauss: Std Err Reverse (bootstrap) =     2.58 kJ/mol\n ========================================================\n\n   Plotting histograms......\n\n   ......done...........\n\n   Execution time = 00:00:10\n\n\nINFO     /tmp/biobb/unitests_167/pmxanalyse/pmxanalyse_log.out:file_utils.py:391 Removed: [&amp;#x27;/tmp/biobb/unitests_167/pmxanalyse/sandbox_d5a33a94-c627-4f23-ac7c-6c775f29a832&amp;#x27;, &amp;#x27;851c5317-7a22-4489-9f12-93a8bf8e40d0&amp;#x27;, &amp;#x27;fe85eda2-45b4-46f7-b5a7-9588f43324f4&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_167\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 -----------------------------\n2024-06-14 18:54:22,706 [MainThread  ] [INFO ]  Executing biobb_pmx.pmxbiobb.pmxatom_mapping Version: 4.2.1\n2024-06-14 18:54:22,706 [MainThread  ] [INFO ]  /tmp/biobb/unitests_167/pmxatom_mapping/sandbox_7abb00ba-2de2-4744-a81e-c55ad98196c0 directory successfully created\n2024-06-14 18:54:22,707 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/lig1.pdb to /tmp/biobb/unitests_167/pmxatom_mapping/sandbox_7abb00ba-2de2-4744-a81e-c55ad98196c0\n2024-06-14 18:54:22,707 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/lig2.pdb to /tmp/biobb/unitests_167/pmxatom_mapping/sandbox_7abb00ba-2de2-4744-a81e-c55ad98196c0\n2024-06-14 18:54:22,707 [MainThread  ] [INFO ]  pmx atomMapping -i1 /tmp/biobb/unitests_167/pmxatom_mapping/sandbox_7abb00ba-2de2-4744-a81e-c55ad98196c0/lig1.pdb -i2 /tmp/biobb/unitests_167/pmxatom_mapping/sandbox_7abb00ba-2de2-4744-a81e-c55ad98196c0/lig2.pdb -o1 /tmp/biobb/unitests_167/pmxatom_mapping/sandbox_7abb00ba-2de2-4744-a81e-c55ad98196c0/pairs1.dat -o2 /tmp/biobb/unitests_167/pmxatom_mapping/sandbox_7abb00ba-2de2-4744-a81e-c55ad98196c0/pairs2.dat -log /tmp/biobb/unitests_167/pmxatom_mapping/sandbox_7abb00ba-2de2-4744-a81e-c55ad98196c0/atom_mapping.log --d 0.05\n\n2024-06-14 18:54:27,198 [MainThread  ] [INFO ]  Exit code 0\n\n2024-06-14 18:54:27,198 [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\n2024-06-14 18:54:27,199 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_167/pmxatom_mapping/sandbox_7abb00ba-2de2-4744-a81e-c55ad98196c0&amp;#x27;]\nChecking if empty file: /tmp/biobb/unitests_167/pmxatom_mapping/pairs1.dat\nChecking if empty file: /tmp/biobb/unitests_167/pmxatom_mapping/pairs2.dat\nComparing: \n        File_A: /tmp/biobb/unitests_167/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_167/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_167/pmxatom_mapping/pmxatom_mapping_log.out:file_utils.py:391 Executing biobb_pmx.pmxbiobb.pmxatom_mapping Version: 4.2.1\nINFO     /tmp/biobb/unitests_167/pmxatom_mapping/pmxatom_mapping_log.out:file_utils.py:82 /tmp/biobb/unitests_167/pmxatom_mapping/sandbox_7abb00ba-2de2-4744-a81e-c55ad98196c0 directory successfully created\nINFO     /tmp/biobb/unitests_167/pmxatom_mapping/pmxatom_mapping_log.out:file_utils.py:391 Copy: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/lig1.pdb to /tmp/biobb/unitests_167/pmxatom_mapping/sandbox_7abb00ba-2de2-4744-a81e-c55ad98196c0\nINFO     /tmp/biobb/unitests_167/pmxatom_mapping/pmxatom_mapping_log.out:file_utils.py:391 Copy: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/lig2.pdb to /tmp/biobb/unitests_167/pmxatom_mapping/sandbox_7abb00ba-2de2-4744-a81e-c55ad98196c0\nINFO     /tmp/biobb/unitests_167/pmxatom_mapping/pmxatom_mapping_log.out:cmd_wrapper.py:33 pmx atomMapping -i1 /tmp/biobb/unitests_167/pmxatom_mapping/sandbox_7abb00ba-2de2-4744-a81e-c55ad98196c0/lig1.pdb -i2 /tmp/biobb/unitests_167/pmxatom_mapping/sandbox_7abb00ba-2de2-4744-a81e-c55ad98196c0/lig2.pdb -o1 /tmp/biobb/unitests_167/pmxatom_mapping/sandbox_7abb00ba-2de2-4744-a81e-c55ad98196c0/pairs1.dat -o2 /tmp/biobb/unitests_167/pmxatom_mapping/sandbox_7abb00ba-2de2-4744-a81e-c55ad98196c0/pairs2.dat -log /tmp/biobb/unitests_167/pmxatom_mapping/sandbox_7abb00ba-2de2-4744-a81e-c55ad98196c0/atom_mapping.log --d 0.05\n\nINFO     /tmp/biobb/unitests_167/pmxatom_mapping/pmxatom_mapping_log.out:cmd_wrapper.py:50 Exit code 0\n\nINFO     /tmp/biobb/unitests_167/pmxatom_mapping/pmxatom_mapping_log.out:cmd_wrapper.py:52 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_167/pmxatom_mapping/pmxatom_mapping_log.out:file_utils.py:391 Removed: [&amp;#x27;/tmp/biobb/unitests_167/pmxatom_mapping/sandbox_7abb00ba-2de2-4744-a81e-c55ad98196c0&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_167\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 -----------------------------\n2024-06-14 18:54:27,232 [MainThread  ] [INFO ]  Executing biobb_pmx.pmxbiobb.pmxcreate_top Version: 4.2.1\n2024-06-14 18:54:27,233 [MainThread  ] [INFO ]  /tmp/biobb/unitests_167/pmxcreate_top/sandbox_08b34f89-6faa-442f-8b0d-360ee8250ba2 directory successfully created\n2024-06-14 18:54:27,233 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/topo1.itp to /tmp/biobb/unitests_167/pmxcreate_top/sandbox_08b34f89-6faa-442f-8b0d-360ee8250ba2\n2024-06-14 18:54:27,233 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/topo2.itp to /tmp/biobb/unitests_167/pmxcreate_top/sandbox_08b34f89-6faa-442f-8b0d-360ee8250ba2\n2024-06-14 18:54:27,233 [MainThread  ] [INFO ]  Running create_top from pmx package...\n\n2024-06-14 18:54:27,234 [MainThread  ] [INFO ]  Creating ae10f009-bafc-4676-946f-54d507587fbb temporary folder\n2024-06-14 18:54:27,234 [MainThread  ] [INFO ]  Creating topo1.itp itp file in temporary folder\n2024-06-14 18:54:27,234 [MainThread  ] [INFO ]  Creating topo2.itp itp file in temporary folder\n2024-06-14 18:54:27,234 [MainThread  ] [INFO ]  Compressing topology to: /tmp/biobb/unitests_167/pmxcreate_top/topo.zip\n2024-06-14 18:54:27,235 [MainThread  ] [INFO ]  Ignored file amber99sb-star-ildn-mut.ff/forcefield.itp\n2024-06-14 18:54:27,235 [MainThread  ] [INFO ]  Ignored file amber99sb-star-ildn-mut.ff/spce.itp\n2024-06-14 18:54:27,235 [MainThread  ] [INFO ]  Ignored file amber99sb-star-ildn-mut.ff/ions.itp\n2024-06-14 18:54:27,236 [MainThread  ] [INFO ]  Adding:\n2024-06-14 18:54:27,236 [MainThread  ] [INFO ]  [&amp;#x27;topo1.itp&amp;#x27;, &amp;#x27;topo2.itp&amp;#x27;, &amp;#x27;topology.top&amp;#x27;]\n2024-06-14 18:54:27,236 [MainThread  ] [INFO ]  to: /tmp/biobb/unitests_167/pmxcreate_top/topo.zip\n2024-06-14 18:54:27,236 [MainThread  ] [INFO ]  Removed: [&amp;#x27;topo1.itp&amp;#x27;, &amp;#x27;topo2.itp&amp;#x27;, &amp;#x27;topology.top&amp;#x27;]\n2024-06-14 18:54:27,236 [MainThread  ] [INFO ]  Exit code 0\n\n2024-06-14 18:54:27,237 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_167/pmxcreate_top/sandbox_08b34f89-6faa-442f-8b0d-360ee8250ba2&amp;#x27;]\nChecking if empty file: /tmp/biobb/unitests_167/pmxcreate_top/topo.zip\nThis is a ZIP comparison!\nUnzipping:\nCreating a unique_dir for: /tmp/biobb/unitests_167/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: 513328a8-9770-4306-96bc-5fcbfc2685a7/topo1.itp\n     FILE_B: 1a72f611-e960-420e-b901-2cb28e34b022/topo1.itp\nComparing TOP/ITP:\n     FILE_A: 513328a8-9770-4306-96bc-5fcbfc2685a7/topo2.itp\n     FILE_B: 1a72f611-e960-420e-b901-2cb28e34b022/topo2.itp\nComparing TOP/ITP:\n     FILE_A: 513328a8-9770-4306-96bc-5fcbfc2685a7/topology.top\n     FILE_B: 1a72f611-e960-420e-b901-2cb28e34b022/topology.top\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_167/pmxcreate_top/pmxcreate_top_log.out:file_utils.py:391 Executing biobb_pmx.pmxbiobb.pmxcreate_top Version: 4.2.1\nINFO     /tmp/biobb/unitests_167/pmxcreate_top/pmxcreate_top_log.out:file_utils.py:82 /tmp/biobb/unitests_167/pmxcreate_top/sandbox_08b34f89-6faa-442f-8b0d-360ee8250ba2 directory successfully created\nINFO     /tmp/biobb/unitests_167/pmxcreate_top/pmxcreate_top_log.out:file_utils.py:391 Copy: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/topo1.itp to /tmp/biobb/unitests_167/pmxcreate_top/sandbox_08b34f89-6faa-442f-8b0d-360ee8250ba2\nINFO     /tmp/biobb/unitests_167/pmxcreate_top/pmxcreate_top_log.out:file_utils.py:391 Copy: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/topo2.itp to /tmp/biobb/unitests_167/pmxcreate_top/sandbox_08b34f89-6faa-442f-8b0d-360ee8250ba2\nINFO     /tmp/biobb/unitests_167/pmxcreate_top/pmxcreate_top_log.out:file_utils.py:391 Running create_top from pmx package...\n\nINFO     /tmp/biobb/unitests_167/pmxcreate_top/pmxcreate_top_log.out:file_utils.py:391 Creating ae10f009-bafc-4676-946f-54d507587fbb temporary folder\nINFO     /tmp/biobb/unitests_167/pmxcreate_top/pmxcreate_top_log.out:file_utils.py:391 Creating topo1.itp itp file in temporary folder\nINFO     /tmp/biobb/unitests_167/pmxcreate_top/pmxcreate_top_log.out:file_utils.py:391 Creating topo2.itp itp file in temporary folder\nINFO     /tmp/biobb/unitests_167/pmxcreate_top/pmxcreate_top_log.out:file_utils.py:391 Compressing topology to: /tmp/biobb/unitests_167/pmxcreate_top/topo.zip\nINFO     /tmp/biobb/unitests_167/pmxcreate_top/pmxcreate_top_log.out:file_utils.py:203 Ignored file amber99sb-star-ildn-mut.ff/forcefield.itp\nINFO     /tmp/biobb/unitests_167/pmxcreate_top/pmxcreate_top_log.out:file_utils.py:203 Ignored file amber99sb-star-ildn-mut.ff/spce.itp\nINFO     /tmp/biobb/unitests_167/pmxcreate_top/pmxcreate_top_log.out:file_utils.py:203 Ignored file amber99sb-star-ildn-mut.ff/ions.itp\nINFO     /tmp/biobb/unitests_167/pmxcreate_top/pmxcreate_top_log.out:file_utils.py:148 Adding:\nINFO     /tmp/biobb/unitests_167/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_167/pmxcreate_top/pmxcreate_top_log.out:file_utils.py:150 to: /tmp/biobb/unitests_167/pmxcreate_top/topo.zip\nINFO     /tmp/biobb/unitests_167/pmxcreate_top/pmxcreate_top_log.out:file_utils.py:391 Removed: [&amp;#x27;topo1.itp&amp;#x27;, &amp;#x27;topo2.itp&amp;#x27;, &amp;#x27;topology.top&amp;#x27;]\nINFO     /tmp/biobb/unitests_167/pmxcreate_top/pmxcreate_top_log.out:file_utils.py:391 Exit code 0\n\nINFO     /tmp/biobb/unitests_167/pmxcreate_top/pmxcreate_top_log.out:file_utils.py:391 Removed: [&amp;#x27;/tmp/biobb/unitests_167/pmxcreate_top/sandbox_08b34f89-6faa-442f-8b0d-360ee8250ba2&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_167\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;00:00:08&#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;00:00:08&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-06-14 18:54:27,275 [MainThread  ] [INFO ]  Executing biobb_pmx.pmxbiobb.pmxgentop Version: 4.2.1\n2024-06-14 18:54:27,275 [MainThread  ] [INFO ]  /tmp/biobb/unitests_167/pmxgentop/sandbox_543b3484-3e9a-42c1-b357-7f6d8bf7bef1 directory successfully created\n2024-06-14 18:54:27,277 [MainThread  ] [INFO ]  Extracting: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/mut_gmx.top.zip\n2024-06-14 18:54:27,277 [MainThread  ] [INFO ]  to:\n2024-06-14 18:54:27,277 [MainThread  ] [INFO ]  [&amp;#x27;9da669df-0f43-44f5-8479-60743e0a650d/p2g.top&amp;#x27;, &amp;#x27;9da669df-0f43-44f5-8479-60743e0a650d/p2g_Ion.itp&amp;#x27;, &amp;#x27;9da669df-0f43-44f5-8479-60743e0a650d/p2g_Protein_chain_A.itp&amp;#x27;, &amp;#x27;9da669df-0f43-44f5-8479-60743e0a650d/posre_Ion.itp&amp;#x27;, &amp;#x27;9da669df-0f43-44f5-8479-60743e0a650d/posre_Protein_chain_A.itp&amp;#x27;]\n2024-06-14 18:54:27,277 [MainThread  ] [INFO ]  Unzipping: \n2024-06-14 18:54:27,277 [MainThread  ] [INFO ]  /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/mut_gmx.top.zip\n2024-06-14 18:54:27,277 [MainThread  ] [INFO ]  To: \n2024-06-14 18:54:27,278 [MainThread  ] [INFO ]  9da669df-0f43-44f5-8479-60743e0a650d/p2g.top\n2024-06-14 18:54:27,278 [MainThread  ] [INFO ]  9da669df-0f43-44f5-8479-60743e0a650d/p2g_Ion.itp\n2024-06-14 18:54:27,278 [MainThread  ] [INFO ]  9da669df-0f43-44f5-8479-60743e0a650d/p2g_Protein_chain_A.itp\n2024-06-14 18:54:27,278 [MainThread  ] [INFO ]  9da669df-0f43-44f5-8479-60743e0a650d/posre_Ion.itp\n2024-06-14 18:54:27,278 [MainThread  ] [INFO ]  9da669df-0f43-44f5-8479-60743e0a650d/posre_Protein_chain_A.itp\n2024-06-14 18:54:27,278 [MainThread  ] [INFO ]  unique_dir_output_file: 81e8ee5f-2a69-4b66-ac0d-5eec1c2e95c9/pmxgentop_p2g.top\n2024-06-14 18:54:27,278 [MainThread  ] [INFO ]  pmx gentop -o 81e8ee5f-2a69-4b66-ac0d-5eec1c2e95c9/pmxgentop_p2g.top -ff amber99sb-star-ildn-mut -p 9da669df-0f43-44f5-8479-60743e0a650d/p2g.top\n\n2024-06-14 18:54:34,470 [MainThread  ] [INFO ]  Exit code 0\n\n2024-06-14 18:54:34,471 [MainThread  ] [INFO ]  \nlog_&amp;gt; Reading input top file &amp;quot;9da669df-0f43-44f5-8479-60743e0a650d/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_167/pmxgentop/81e8ee5f-2a69-4b66-ac0d-5eec1c2e95c9/pmx_p2g_Protein_chain_A.itp&amp;quot;&amp;quot;\n\nlog_&amp;gt; Writing itp file &amp;quot;/tmp/biobb/unitests_167/pmxgentop/81e8ee5f-2a69-4b66-ac0d-5eec1c2e95c9/pmx_p2g_Ion.itp&amp;quot;&amp;quot;\n\nlog_&amp;gt; Writing topology file &amp;quot;81e8ee5f-2a69-4b66-ac0d-5eec1c2e95c9/pmxgentop_p2g.top&amp;quot;&amp;quot;\n\nb-states filled...........\n\n\n2024-06-14 18:54:35,317 [MainThread  ] [INFO ]  Check if 81e8ee5f-2a69-4b66-ac0d-5eec1c2e95c9/p2g_Protein_chain_A.itp exists\n2024-06-14 18:54:35,318 [MainThread  ] [INFO ]  Copying 9da669df-0f43-44f5-8479-60743e0a650d/p2g_Protein_chain_A.itp to: 81e8ee5f-2a69-4b66-ac0d-5eec1c2e95c9\n2024-06-14 18:54:35,318 [MainThread  ] [INFO ]  Check if 81e8ee5f-2a69-4b66-ac0d-5eec1c2e95c9/p2g_Ion.itp exists\n2024-06-14 18:54:35,319 [MainThread  ] [INFO ]  Copying 9da669df-0f43-44f5-8479-60743e0a650d/p2g_Ion.itp to: 81e8ee5f-2a69-4b66-ac0d-5eec1c2e95c9\n2024-06-14 18:54:35,319 [MainThread  ] [INFO ]  Check if 81e8ee5f-2a69-4b66-ac0d-5eec1c2e95c9/p2g.top exists\n2024-06-14 18:54:35,319 [MainThread  ] [INFO ]  Copying 9da669df-0f43-44f5-8479-60743e0a650d/p2g.top to: 81e8ee5f-2a69-4b66-ac0d-5eec1c2e95c9\n2024-06-14 18:54:35,319 [MainThread  ] [INFO ]  Check if 81e8ee5f-2a69-4b66-ac0d-5eec1c2e95c9/posre_Protein_chain_A.itp exists\n2024-06-14 18:54:35,319 [MainThread  ] [INFO ]  Copying 9da669df-0f43-44f5-8479-60743e0a650d/posre_Protein_chain_A.itp to: 81e8ee5f-2a69-4b66-ac0d-5eec1c2e95c9\n2024-06-14 18:54:35,320 [MainThread  ] [INFO ]  Check if 81e8ee5f-2a69-4b66-ac0d-5eec1c2e95c9/posre_Ion.itp exists\n2024-06-14 18:54:35,320 [MainThread  ] [INFO ]  Copying 9da669df-0f43-44f5-8479-60743e0a650d/posre_Ion.itp to: 81e8ee5f-2a69-4b66-ac0d-5eec1c2e95c9\n2024-06-14 18:54:35,320 [MainThread  ] [INFO ]  Compressing topology to: /tmp/biobb/unitests_167/pmxgentop/output_topology.zip\n2024-06-14 18:54:35,320 [MainThread  ] [INFO ]  Ignored file 81e8ee5f-2a69-4b66-ac0d-5eec1c2e95c9/amber99sb-star-ildn-mut.ff/forcefield.itp\n2024-06-14 18:54:35,505 [MainThread  ] [INFO ]  Ignored file 81e8ee5f-2a69-4b66-ac0d-5eec1c2e95c9/amber99sb-star-ildn-mut.ff/spce.itp\n2024-06-14 18:54:35,505 [MainThread  ] [INFO ]  Ignored file 81e8ee5f-2a69-4b66-ac0d-5eec1c2e95c9/amber99sb-star-ildn-mut.ff/ions.itp\n2024-06-14 18:54:35,507 [MainThread  ] [INFO ]  Adding:\n2024-06-14 18:54:35,508 [MainThread  ] [INFO ]  [&amp;#x27;81e8ee5f-2a69-4b66-ac0d-5eec1c2e95c9/pmx_p2g_Ion.itp&amp;#x27;, &amp;#x27;81e8ee5f-2a69-4b66-ac0d-5eec1c2e95c9/pmx_p2g_Protein_chain_A.itp&amp;#x27;, &amp;#x27;81e8ee5f-2a69-4b66-ac0d-5eec1c2e95c9/pmxgentop_p2g.top&amp;#x27;, &amp;#x27;81e8ee5f-2a69-4b66-ac0d-5eec1c2e95c9/posre_Ion.itp&amp;#x27;, &amp;#x27;81e8ee5f-2a69-4b66-ac0d-5eec1c2e95c9/posre_Protein_chain_A.itp&amp;#x27;]\n2024-06-14 18:54:35,508 [MainThread  ] [INFO ]  to: /tmp/biobb/unitests_167/pmxgentop/output_topology.zip\n2024-06-14 18:54:35,508 [MainThread  ] [INFO ]  Removed: [&amp;#x27;81e8ee5f-2a69-4b66-ac0d-5eec1c2e95c9/posre_Protein_chain_A.itp&amp;#x27;, &amp;#x27;81e8ee5f-2a69-4b66-ac0d-5eec1c2e95c9/pmx_p2g_Protein_chain_A.itp&amp;#x27;, &amp;#x27;81e8ee5f-2a69-4b66-ac0d-5eec1c2e95c9/posre_Ion.itp&amp;#x27;, &amp;#x27;81e8ee5f-2a69-4b66-ac0d-5eec1c2e95c9/pmx_p2g_Ion.itp&amp;#x27;, &amp;#x27;81e8ee5f-2a69-4b66-ac0d-5eec1c2e95c9/pmxgentop_p2g.top&amp;#x27;]\nChecking if empty file: /tmp/biobb/unitests_167/pmxgentop/output_topology.zip\nThis is a ZIP comparison!\nUnzipping:\nCreating a unique_dir for: /tmp/biobb/unitests_167/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: 2fa37661-89c6-4a29-bc36-586a391586e6/pmx_p2g_Ion.itp\n     FILE_B: c4e00aa7-ef16-496a-ae58-17b402a9edbe/pmx_p2g_Ion.itp\nComparing TOP/ITP:\n     FILE_A: 2fa37661-89c6-4a29-bc36-586a391586e6/pmx_p2g_Protein_chain_A.itp\n     FILE_B: c4e00aa7-ef16-496a-ae58-17b402a9edbe/pmx_p2g_Protein_chain_A.itp\nComparing TOP/ITP:\n     FILE_A: 2fa37661-89c6-4a29-bc36-586a391586e6/pmxgentop_p2g.top\n     FILE_B: c4e00aa7-ef16-496a-ae58-17b402a9edbe/pmxgentop_p2g.top\nComparing TOP/ITP:\n     FILE_A: 2fa37661-89c6-4a29-bc36-586a391586e6/posre_Ion.itp\n     FILE_B: c4e00aa7-ef16-496a-ae58-17b402a9edbe/posre_Ion.itp\nComparing TOP/ITP:\n     FILE_A: 2fa37661-89c6-4a29-bc36-586a391586e6/posre_Protein_chain_A.itp\n     FILE_B: c4e00aa7-ef16-496a-ae58-17b402a9edbe/posre_Protein_chain_A.itp\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_167/pmxgentop/pmxgentop_log.out:file_utils.py:391 Executing biobb_pmx.pmxbiobb.pmxgentop Version: 4.2.1\nINFO     /tmp/biobb/unitests_167/pmxgentop/pmxgentop_log.out:file_utils.py:82 /tmp/biobb/unitests_167/pmxgentop/sandbox_543b3484-3e9a-42c1-b357-7f6d8bf7bef1 directory successfully created\nINFO     /tmp/biobb/unitests_167/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_167/pmxgentop/pmxgentop_log.out:file_utils.py:173 to:\nINFO     /tmp/biobb/unitests_167/pmxgentop/pmxgentop_log.out:file_utils.py:174 [&amp;#x27;9da669df-0f43-44f5-8479-60743e0a650d/p2g.top&amp;#x27;, &amp;#x27;9da669df-0f43-44f5-8479-60743e0a650d/p2g_Ion.itp&amp;#x27;, &amp;#x27;9da669df-0f43-44f5-8479-60743e0a650d/p2g_Protein_chain_A.itp&amp;#x27;, &amp;#x27;9da669df-0f43-44f5-8479-60743e0a650d/posre_Ion.itp&amp;#x27;, &amp;#x27;9da669df-0f43-44f5-8479-60743e0a650d/posre_Protein_chain_A.itp&amp;#x27;]\nINFO     /tmp/biobb/unitests_167/pmxgentop/pmxgentop_log.out:file_utils.py:252 Unzipping: \nINFO     /tmp/biobb/unitests_167/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_167/pmxgentop/pmxgentop_log.out:file_utils.py:254 To: \nINFO     /tmp/biobb/unitests_167/pmxgentop/pmxgentop_log.out:file_utils.py:256 9da669df-0f43-44f5-8479-60743e0a650d/p2g.top\nINFO     /tmp/biobb/unitests_167/pmxgentop/pmxgentop_log.out:file_utils.py:256 9da669df-0f43-44f5-8479-60743e0a650d/p2g_Ion.itp\nINFO     /tmp/biobb/unitests_167/pmxgentop/pmxgentop_log.out:file_utils.py:256 9da669df-0f43-44f5-8479-60743e0a650d/p2g_Protein_chain_A.itp\nINFO     /tmp/biobb/unitests_167/pmxgentop/pmxgentop_log.out:file_utils.py:256 9da669df-0f43-44f5-8479-60743e0a650d/posre_Ion.itp\nINFO     /tmp/biobb/unitests_167/pmxgentop/pmxgentop_log.out:file_utils.py:256 9da669df-0f43-44f5-8479-60743e0a650d/posre_Protein_chain_A.itp\nINFO     /tmp/biobb/unitests_167/pmxgentop/pmxgentop_log.out:file_utils.py:391 unique_dir_output_file: 81e8ee5f-2a69-4b66-ac0d-5eec1c2e95c9/pmxgentop_p2g.top\nINFO     /tmp/biobb/unitests_167/pmxgentop/pmxgentop_log.out:cmd_wrapper.py:33 pmx gentop -o 81e8ee5f-2a69-4b66-ac0d-5eec1c2e95c9/pmxgentop_p2g.top -ff amber99sb-star-ildn-mut -p 9da669df-0f43-44f5-8479-60743e0a650d/p2g.top\n\nINFO     /tmp/biobb/unitests_167/pmxgentop/pmxgentop_log.out:cmd_wrapper.py:50 Exit code 0\n\nINFO     /tmp/biobb/unitests_167/pmxgentop/pmxgentop_log.out:cmd_wrapper.py:52 \nlog_&amp;gt; Reading input top file &amp;quot;9da669df-0f43-44f5-8479-60743e0a650d/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_167/pmxgentop/81e8ee5f-2a69-4b66-ac0d-5eec1c2e95c9/pmx_p2g_Protein_chain_A.itp&amp;quot;&amp;quot;\n\nlog_&amp;gt; Writing itp file &amp;quot;/tmp/biobb/unitests_167/pmxgentop/81e8ee5f-2a69-4b66-ac0d-5eec1c2e95c9/pmx_p2g_Ion.itp&amp;quot;&amp;quot;\n\nlog_&amp;gt; Writing topology file &amp;quot;81e8ee5f-2a69-4b66-ac0d-5eec1c2e95c9/pmxgentop_p2g.top&amp;quot;&amp;quot;\n\nb-states filled...........\n\n\nINFO     /tmp/biobb/unitests_167/pmxgentop/pmxgentop_log.out:file_utils.py:391 Check if 81e8ee5f-2a69-4b66-ac0d-5eec1c2e95c9/p2g_Protein_chain_A.itp exists\nINFO     /tmp/biobb/unitests_167/pmxgentop/pmxgentop_log.out:file_utils.py:391 Copying 9da669df-0f43-44f5-8479-60743e0a650d/p2g_Protein_chain_A.itp to: 81e8ee5f-2a69-4b66-ac0d-5eec1c2e95c9\nINFO     /tmp/biobb/unitests_167/pmxgentop/pmxgentop_log.out:file_utils.py:391 Check if 81e8ee5f-2a69-4b66-ac0d-5eec1c2e95c9/p2g_Ion.itp exists\nINFO     /tmp/biobb/unitests_167/pmxgentop/pmxgentop_log.out:file_utils.py:391 Copying 9da669df-0f43-44f5-8479-60743e0a650d/p2g_Ion.itp to: 81e8ee5f-2a69-4b66-ac0d-5eec1c2e95c9\nINFO     /tmp/biobb/unitests_167/pmxgentop/pmxgentop_log.out:file_utils.py:391 Check if 81e8ee5f-2a69-4b66-ac0d-5eec1c2e95c9/p2g.top exists\nINFO     /tmp/biobb/unitests_167/pmxgentop/pmxgentop_log.out:file_utils.py:391 Copying 9da669df-0f43-44f5-8479-60743e0a650d/p2g.top to: 81e8ee5f-2a69-4b66-ac0d-5eec1c2e95c9\nINFO     /tmp/biobb/unitests_167/pmxgentop/pmxgentop_log.out:file_utils.py:391 Check if 81e8ee5f-2a69-4b66-ac0d-5eec1c2e95c9/posre_Protein_chain_A.itp exists\nINFO     /tmp/biobb/unitests_167/pmxgentop/pmxgentop_log.out:file_utils.py:391 Copying 9da669df-0f43-44f5-8479-60743e0a650d/posre_Protein_chain_A.itp to: 81e8ee5f-2a69-4b66-ac0d-5eec1c2e95c9\nINFO     /tmp/biobb/unitests_167/pmxgentop/pmxgentop_log.out:file_utils.py:391 Check if 81e8ee5f-2a69-4b66-ac0d-5eec1c2e95c9/posre_Ion.itp exists\nINFO     /tmp/biobb/unitests_167/pmxgentop/pmxgentop_log.out:file_utils.py:391 Copying 9da669df-0f43-44f5-8479-60743e0a650d/posre_Ion.itp to: 81e8ee5f-2a69-4b66-ac0d-5eec1c2e95c9\nINFO     /tmp/biobb/unitests_167/pmxgentop/pmxgentop_log.out:file_utils.py:391 Compressing topology to: /tmp/biobb/unitests_167/pmxgentop/output_topology.zip\nINFO     /tmp/biobb/unitests_167/pmxgentop/pmxgentop_log.out:file_utils.py:203 Ignored file 81e8ee5f-2a69-4b66-ac0d-5eec1c2e95c9/amber99sb-star-ildn-mut.ff/forcefield.itp\nINFO     /tmp/biobb/unitests_167/pmxgentop/pmxgentop_log.out:file_utils.py:203 Ignored file 81e8ee5f-2a69-4b66-ac0d-5eec1c2e95c9/amber99sb-star-ildn-mut.ff/spce.itp\nINFO     /tmp/biobb/unitests_167/pmxgentop/pmxgentop_log.out:file_utils.py:203 Ignored file 81e8ee5f-2a69-4b66-ac0d-5eec1c2e95c9/amber99sb-star-ildn-mut.ff/ions.itp\nINFO     /tmp/biobb/unitests_167/pmxgentop/pmxgentop_log.out:file_utils.py:148 Adding:\nINFO     /tmp/biobb/unitests_167/pmxgentop/pmxgentop_log.out:file_utils.py:149 [&amp;#x27;81e8ee5f-2a69-4b66-ac0d-5eec1c2e95c9/pmx_p2g_Ion.itp&amp;#x27;, &amp;#x27;81e8ee5f-2a69-4b66-ac0d-5eec1c2e95c9/pmx_p2g_Protein_chain_A.itp&amp;#x27;, &amp;#x27;81e8ee5f-2a69-4b66-ac0d-5eec1c2e95c9/pmxgentop_p2g.top&amp;#x27;, &amp;#x27;81e8ee5f-2a69-4b66-ac0d-5eec1c2e95c9/posre_Ion.itp&amp;#x27;, &amp;#x27;81e8ee5f-2a69-4b66-ac0d-5eec1c2e95c9/posre_Protein_chain_A.itp&amp;#x27;]\nINFO     /tmp/biobb/unitests_167/pmxgentop/pmxgentop_log.out:file_utils.py:150 to: /tmp/biobb/unitests_167/pmxgentop/output_topology.zip\nINFO     /tmp/biobb/unitests_167/pmxgentop/pmxgentop_log.out:file_utils.py:391 Removed: [&amp;#x27;81e8ee5f-2a69-4b66-ac0d-5eec1c2e95c9/posre_Protein_chain_A.itp&amp;#x27;, &amp;#x27;81e8ee5f-2a69-4b66-ac0d-5eec1c2e95c9/pmx_p2g_Protein_chain_A.itp&amp;#x27;, &amp;#x27;81e8ee5f-2a69-4b66-ac0d-5eec1c2e95c9/posre_Ion.itp&amp;#x27;, &amp;#x27;81e8ee5f-2a69-4b66-ac0d-5eec1c2e95c9/pmx_p2g_Ion.itp&amp;#x27;, &amp;#x27;81e8ee5f-2a69-4b66-ac0d-5eec1c2e95c9/pmxgentop_p2g.top&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_167\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 -----------------------------\n2024-06-14 18:54:35,717 [MainThread  ] [INFO ]  Executing biobb_pmx.pmxbiobb.pmxligand_hybrid Version: 4.2.1\n2024-06-14 18:54:35,717 [MainThread  ] [INFO ]  /tmp/biobb/unitests_167/pmxligand_hybrid/sandbox_0c3502fb-20ac-4e6f-b5fb-080af474101b directory successfully created\n2024-06-14 18:54:35,718 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/lig1.pdb to /tmp/biobb/unitests_167/pmxligand_hybrid/sandbox_0c3502fb-20ac-4e6f-b5fb-080af474101b\n2024-06-14 18:54:35,718 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/lig2.pdb to /tmp/biobb/unitests_167/pmxligand_hybrid/sandbox_0c3502fb-20ac-4e6f-b5fb-080af474101b\n2024-06-14 18:54:35,718 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/topoLig1.itp to /tmp/biobb/unitests_167/pmxligand_hybrid/sandbox_0c3502fb-20ac-4e6f-b5fb-080af474101b\n2024-06-14 18:54:35,718 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/topoLig2.itp to /tmp/biobb/unitests_167/pmxligand_hybrid/sandbox_0c3502fb-20ac-4e6f-b5fb-080af474101b\n2024-06-14 18:54:35,719 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/myPairs1.dat to /tmp/biobb/unitests_167/pmxligand_hybrid/sandbox_0c3502fb-20ac-4e6f-b5fb-080af474101b\n2024-06-14 18:54:35,719 [MainThread  ] [INFO ]  pmx ligandHybrid -i1 /tmp/biobb/unitests_167/pmxligand_hybrid/sandbox_0c3502fb-20ac-4e6f-b5fb-080af474101b/lig1.pdb -i2 /tmp/biobb/unitests_167/pmxligand_hybrid/sandbox_0c3502fb-20ac-4e6f-b5fb-080af474101b/lig2.pdb -itp1 /tmp/biobb/unitests_167/pmxligand_hybrid/sandbox_0c3502fb-20ac-4e6f-b5fb-080af474101b/topoLig1.itp -itp2 /tmp/biobb/unitests_167/pmxligand_hybrid/sandbox_0c3502fb-20ac-4e6f-b5fb-080af474101b/topoLig2.itp -pairs /tmp/biobb/unitests_167/pmxligand_hybrid/sandbox_0c3502fb-20ac-4e6f-b5fb-080af474101b/myPairs1.dat -oA /tmp/biobb/unitests_167/pmxligand_hybrid/sandbox_0c3502fb-20ac-4e6f-b5fb-080af474101b/hybridStruct1.pdb -oB /tmp/biobb/unitests_167/pmxligand_hybrid/sandbox_0c3502fb-20ac-4e6f-b5fb-080af474101b/hybridStruct2.pdb -oitp /tmp/biobb/unitests_167/pmxligand_hybrid/sandbox_0c3502fb-20ac-4e6f-b5fb-080af474101b/hybridTopo.itp -offitp /tmp/biobb/unitests_167/pmxligand_hybrid/sandbox_0c3502fb-20ac-4e6f-b5fb-080af474101b/hybridAtomTypes.itp -log /tmp/biobb/unitests_167/pmxligand_hybrid/sandbox_0c3502fb-20ac-4e6f-b5fb-080af474101b/ligand_hybrid.log --fit --d 0.05\n\n2024-06-14 18:54:37,345 [MainThread  ] [INFO ]  Exit code 0\n\n2024-06-14 18:54:37,345 [MainThread  ] [INFO ]  ligandHybridTop__log_&amp;gt; Reading ligand 1 from: &amp;quot;/tmp/biobb/unitests_167/pmxligand_hybrid/sandbox_0c3502fb-20ac-4e6f-b5fb-080af474101b/lig1.pdb&amp;quot;\nligandHybridTop__log_&amp;gt; Reading ligand 2 from: &amp;quot;/tmp/biobb/unitests_167/pmxligand_hybrid/sandbox_0c3502fb-20ac-4e6f-b5fb-080af474101b/lig2.pdb&amp;quot;\nligandHybridTop__log_&amp;gt; Reading topology 1 from: &amp;quot;/tmp/biobb/unitests_167/pmxligand_hybrid/sandbox_0c3502fb-20ac-4e6f-b5fb-080af474101b/topoLig1.itp&amp;quot;\nligandHybridTop__log_&amp;gt; Reading topology 2 from: &amp;quot;/tmp/biobb/unitests_167/pmxligand_hybrid/sandbox_0c3502fb-20ac-4e6f-b5fb-080af474101b/topoLig2.itp&amp;quot;\nligandHybridTop__log_&amp;gt; Reading file with atom pairs: &amp;quot;/tmp/biobb/unitests_167/pmxligand_hybrid/sandbox_0c3502fb-20ac-4e6f-b5fb-080af474101b/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_167/pmxligand_hybrid/sandbox_0c3502fb-20ac-4e6f-b5fb-080af474101b/hybridTopo.itp&amp;quot;\nligandHybridTop__log_&amp;gt; Writing dummy forcefield file: &amp;quot;/tmp/biobb/unitests_167/pmxligand_hybrid/sandbox_0c3502fb-20ac-4e6f-b5fb-080af474101b/hybridAtomTypes.itp&amp;quot;\n\n2024-06-14 18:54:37,347 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_167/pmxligand_hybrid/sandbox_0c3502fb-20ac-4e6f-b5fb-080af474101b&amp;#x27;]\nChecking if empty file: /tmp/biobb/unitests_167/pmxligand_hybrid/hybridStruct1.pdb\nChecking if empty file: /tmp/biobb/unitests_167/pmxligand_hybrid/hybridStruct2.pdb\nChecking if empty file: /tmp/biobb/unitests_167/pmxligand_hybrid/hybridTopo.itp\nChecking if empty file: /tmp/biobb/unitests_167/pmxligand_hybrid/hybridAtomTypes.itp\nChecking RMSD between:\n     PDB_A: /tmp/biobb/unitests_167/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_167/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_167/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_167/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_167/pmxligand_hybrid/pmxligand_hybrid_log.out:file_utils.py:391 Executing biobb_pmx.pmxbiobb.pmxligand_hybrid Version: 4.2.1\nINFO     /tmp/biobb/unitests_167/pmxligand_hybrid/pmxligand_hybrid_log.out:file_utils.py:82 /tmp/biobb/unitests_167/pmxligand_hybrid/sandbox_0c3502fb-20ac-4e6f-b5fb-080af474101b directory successfully created\nINFO     /tmp/biobb/unitests_167/pmxligand_hybrid/pmxligand_hybrid_log.out:file_utils.py:391 Copy: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/lig1.pdb to /tmp/biobb/unitests_167/pmxligand_hybrid/sandbox_0c3502fb-20ac-4e6f-b5fb-080af474101b\nINFO     /tmp/biobb/unitests_167/pmxligand_hybrid/pmxligand_hybrid_log.out:file_utils.py:391 Copy: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/lig2.pdb to /tmp/biobb/unitests_167/pmxligand_hybrid/sandbox_0c3502fb-20ac-4e6f-b5fb-080af474101b\nINFO     /tmp/biobb/unitests_167/pmxligand_hybrid/pmxligand_hybrid_log.out:file_utils.py:391 Copy: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/topoLig1.itp to /tmp/biobb/unitests_167/pmxligand_hybrid/sandbox_0c3502fb-20ac-4e6f-b5fb-080af474101b\nINFO     /tmp/biobb/unitests_167/pmxligand_hybrid/pmxligand_hybrid_log.out:file_utils.py:391 Copy: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/topoLig2.itp to /tmp/biobb/unitests_167/pmxligand_hybrid/sandbox_0c3502fb-20ac-4e6f-b5fb-080af474101b\nINFO     /tmp/biobb/unitests_167/pmxligand_hybrid/pmxligand_hybrid_log.out:file_utils.py:391 Copy: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/myPairs1.dat to /tmp/biobb/unitests_167/pmxligand_hybrid/sandbox_0c3502fb-20ac-4e6f-b5fb-080af474101b\nINFO     /tmp/biobb/unitests_167/pmxligand_hybrid/pmxligand_hybrid_log.out:cmd_wrapper.py:33 pmx ligandHybrid -i1 /tmp/biobb/unitests_167/pmxligand_hybrid/sandbox_0c3502fb-20ac-4e6f-b5fb-080af474101b/lig1.pdb -i2 /tmp/biobb/unitests_167/pmxligand_hybrid/sandbox_0c3502fb-20ac-4e6f-b5fb-080af474101b/lig2.pdb -itp1 /tmp/biobb/unitests_167/pmxligand_hybrid/sandbox_0c3502fb-20ac-4e6f-b5fb-080af474101b/topoLig1.itp -itp2 /tmp/biobb/unitests_167/pmxligand_hybrid/sandbox_0c3502fb-20ac-4e6f-b5fb-080af474101b/topoLig2.itp -pairs /tmp/biobb/unitests_167/pmxligand_hybrid/sandbox_0c3502fb-20ac-4e6f-b5fb-080af474101b/myPairs1.dat -oA /tmp/biobb/unitests_167/pmxligand_hybrid/sandbox_0c3502fb-20ac-4e6f-b5fb-080af474101b/hybridStruct1.pdb -oB /tmp/biobb/unitests_167/pmxligand_hybrid/sandbox_0c3502fb-20ac-4e6f-b5fb-080af474101b/hybridStruct2.pdb -oitp /tmp/biobb/unitests_167/pmxligand_hybrid/sandbox_0c3502fb-20ac-4e6f-b5fb-080af474101b/hybridTopo.itp -offitp /tmp/biobb/unitests_167/pmxligand_hybrid/sandbox_0c3502fb-20ac-4e6f-b5fb-080af474101b/hybridAtomTypes.itp -log /tmp/biobb/unitests_167/pmxligand_hybrid/sandbox_0c3502fb-20ac-4e6f-b5fb-080af474101b/ligand_hybrid.log --fit --d 0.05\n\nINFO     /tmp/biobb/unitests_167/pmxligand_hybrid/pmxligand_hybrid_log.out:cmd_wrapper.py:50 Exit code 0\n\nINFO     /tmp/biobb/unitests_167/pmxligand_hybrid/pmxligand_hybrid_log.out:cmd_wrapper.py:52 ligandHybridTop__log_&amp;gt; Reading ligand 1 from: &amp;quot;/tmp/biobb/unitests_167/pmxligand_hybrid/sandbox_0c3502fb-20ac-4e6f-b5fb-080af474101b/lig1.pdb&amp;quot;\nligandHybridTop__log_&amp;gt; Reading ligand 2 from: &amp;quot;/tmp/biobb/unitests_167/pmxligand_hybrid/sandbox_0c3502fb-20ac-4e6f-b5fb-080af474101b/lig2.pdb&amp;quot;\nligandHybridTop__log_&amp;gt; Reading topology 1 from: &amp;quot;/tmp/biobb/unitests_167/pmxligand_hybrid/sandbox_0c3502fb-20ac-4e6f-b5fb-080af474101b/topoLig1.itp&amp;quot;\nligandHybridTop__log_&amp;gt; Reading topology 2 from: &amp;quot;/tmp/biobb/unitests_167/pmxligand_hybrid/sandbox_0c3502fb-20ac-4e6f-b5fb-080af474101b/topoLig2.itp&amp;quot;\nligandHybridTop__log_&amp;gt; Reading file with atom pairs: &amp;quot;/tmp/biobb/unitests_167/pmxligand_hybrid/sandbox_0c3502fb-20ac-4e6f-b5fb-080af474101b/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_167/pmxligand_hybrid/sandbox_0c3502fb-20ac-4e6f-b5fb-080af474101b/hybridTopo.itp&amp;quot;\nligandHybridTop__log_&amp;gt; Writing dummy forcefield file: &amp;quot;/tmp/biobb/unitests_167/pmxligand_hybrid/sandbox_0c3502fb-20ac-4e6f-b5fb-080af474101b/hybridAtomTypes.itp&amp;quot;\n\nINFO     /tmp/biobb/unitests_167/pmxligand_hybrid/pmxligand_hybrid_log.out:file_utils.py:391 Removed: [&amp;#x27;/tmp/biobb/unitests_167/pmxligand_hybrid/sandbox_0c3502fb-20ac-4e6f-b5fb-080af474101b&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_167\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;33 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;33 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 -----------------------------\n2024-06-14 18:54:37,391 [MainThread  ] [INFO ]  Executing biobb_pmx.pmxbiobb.pmxmerge_ff Version: 4.2.1\n2024-06-14 18:54:37,391 [MainThread  ] [INFO ]  /tmp/biobb/unitests_167/pmxmerge_ff/sandbox_67d0881f-ec40-49f9-b25f-53c6293bc1db directory successfully created\n2024-06-14 18:54:37,392 [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_167/pmxmerge_ff/sandbox_67d0881f-ec40-49f9-b25f-53c6293bc1db\n2024-06-14 18:54:37,392 [MainThread  ] [INFO ]  Creating 9c630cc0-efd4-451d-82f4-1fe031df16a1 temporary folder\n2024-06-14 18:54:37,392 [MainThread  ] [INFO ]  Extracting: /tmp/biobb/unitests_167/pmxmerge_ff/sandbox_67d0881f-ec40-49f9-b25f-53c6293bc1db/itps_to_merge.zip\n2024-06-14 18:54:37,393 [MainThread  ] [INFO ]  to:\n2024-06-14 18:54:37,393 [MainThread  ] [INFO ]  [&amp;#x27;9c630cc0-efd4-451d-82f4-1fe031df16a1/myHybridAtomTypes.itp&amp;#x27;, &amp;#x27;9c630cc0-efd4-451d-82f4-1fe031df16a1/lig1ffMOL.itp&amp;#x27;, &amp;#x27;9c630cc0-efd4-451d-82f4-1fe031df16a1/lig2ffMOL.itp&amp;#x27;]\n2024-06-14 18:54:37,393 [MainThread  ] [INFO ]  Running merge_FF_files from pmx package...\n\n2024-06-14 18:54:37,394 [MainThread  ] [INFO ]  Exit code 0\n\n2024-06-14 18:54:37,394 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_167/pmxmerge_ff/sandbox_67d0881f-ec40-49f9-b25f-53c6293bc1db&amp;#x27;]\nChecking if empty file: /tmp/biobb/unitests_167/pmxmerge_ff/hybridTopo.itp\nComparing size of both files:\n     FILE_A: /tmp/biobb/unitests_167/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_167/pmxmerge_ff/pmxmerge_ff_log.out:file_utils.py:391 Executing biobb_pmx.pmxbiobb.pmxmerge_ff Version: 4.2.1\nINFO     /tmp/biobb/unitests_167/pmxmerge_ff/pmxmerge_ff_log.out:file_utils.py:82 /tmp/biobb/unitests_167/pmxmerge_ff/sandbox_67d0881f-ec40-49f9-b25f-53c6293bc1db directory successfully created\nINFO     /tmp/biobb/unitests_167/pmxmerge_ff/pmxmerge_ff_log.out:file_utils.py:391 Copy: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/itps_to_merge.zip to /tmp/biobb/unitests_167/pmxmerge_ff/sandbox_67d0881f-ec40-49f9-b25f-53c6293bc1db\nINFO     /tmp/biobb/unitests_167/pmxmerge_ff/pmxmerge_ff_log.out:file_utils.py:391 Creating 9c630cc0-efd4-451d-82f4-1fe031df16a1 temporary folder\nINFO     /tmp/biobb/unitests_167/pmxmerge_ff/pmxmerge_ff_log.out:file_utils.py:172 Extracting: /tmp/biobb/unitests_167/pmxmerge_ff/sandbox_67d0881f-ec40-49f9-b25f-53c6293bc1db/itps_to_merge.zip\nINFO     /tmp/biobb/unitests_167/pmxmerge_ff/pmxmerge_ff_log.out:file_utils.py:173 to:\nINFO     /tmp/biobb/unitests_167/pmxmerge_ff/pmxmerge_ff_log.out:file_utils.py:174 [&amp;#x27;9c630cc0-efd4-451d-82f4-1fe031df16a1/myHybridAtomTypes.itp&amp;#x27;, &amp;#x27;9c630cc0-efd4-451d-82f4-1fe031df16a1/lig1ffMOL.itp&amp;#x27;, &amp;#x27;9c630cc0-efd4-451d-82f4-1fe031df16a1/lig2ffMOL.itp&amp;#x27;]\nINFO     /tmp/biobb/unitests_167/pmxmerge_ff/pmxmerge_ff_log.out:file_utils.py:391 Running merge_FF_files from pmx package...\n\nINFO     /tmp/biobb/unitests_167/pmxmerge_ff/pmxmerge_ff_log.out:file_utils.py:391 Exit code 0\n\nINFO     /tmp/biobb/unitests_167/pmxmerge_ff/pmxmerge_ff_log.out:file_utils.py:391 Removed: [&amp;#x27;/tmp/biobb/unitests_167/pmxmerge_ff/sandbox_67d0881f-ec40-49f9-b25f-53c6293bc1db&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_167\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 -----------------------------\n2024-06-14 18:54:37,425 [MainThread  ] [INFO ]  Executing biobb_pmx.pmxbiobb.pmxmutate Version: 4.2.1\n2024-06-14 18:54:37,425 [MainThread  ] [INFO ]  /tmp/biobb/unitests_167/pmxmutate/sandbox_30f44023-b099-411f-b053-a691e743ff28 directory successfully created\n2024-06-14 18:54:37,428 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/frameA0.pdb to /tmp/biobb/unitests_167/pmxmutate/sandbox_30f44023-b099-411f-b053-a691e743ff28\n2024-06-14 18:54:37,429 [MainThread  ] [INFO ]  pmx mutate -f /tmp/biobb/unitests_167/pmxmutate/sandbox_30f44023-b099-411f-b053-a691e743ff28/frameA0.pdb -o /tmp/biobb/unitests_167/pmxmutate/sandbox_30f44023-b099-411f-b053-a691e743ff28/output_structure.pdb -ff amber99sb-star-ildn-mut --script 387f1aeb-763f-4f92-9503-a9545a252142/mutations.txt\n\n2024-06-14 18:54:40,212 [MainThread  ] [INFO ]  Exit code 0\n\n2024-06-14 18:54:40,213 [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\n2024-06-14 18:54:40,216 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_167/pmxmutate/sandbox_30f44023-b099-411f-b053-a691e743ff28&amp;#x27;]\nChecking if empty file: /tmp/biobb/unitests_167/pmxmutate/output_structure.pdb\nChecking RMSD between:\n     PDB_A: /tmp/biobb/unitests_167/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_167/pmxmutate/pmxmutate_log.out:file_utils.py:391 Executing biobb_pmx.pmxbiobb.pmxmutate Version: 4.2.1\nINFO     /tmp/biobb/unitests_167/pmxmutate/pmxmutate_log.out:file_utils.py:82 /tmp/biobb/unitests_167/pmxmutate/sandbox_30f44023-b099-411f-b053-a691e743ff28 directory successfully created\nINFO     /tmp/biobb/unitests_167/pmxmutate/pmxmutate_log.out:file_utils.py:391 Copy: /home/user/actions-runner/_work/biobb_pmx/biobb_pmx/biobb_pmx/test/data/pmx/frameA0.pdb to /tmp/biobb/unitests_167/pmxmutate/sandbox_30f44023-b099-411f-b053-a691e743ff28\nINFO     /tmp/biobb/unitests_167/pmxmutate/pmxmutate_log.out:cmd_wrapper.py:33 pmx mutate -f /tmp/biobb/unitests_167/pmxmutate/sandbox_30f44023-b099-411f-b053-a691e743ff28/frameA0.pdb -o /tmp/biobb/unitests_167/pmxmutate/sandbox_30f44023-b099-411f-b053-a691e743ff28/output_structure.pdb -ff amber99sb-star-ildn-mut --script 387f1aeb-763f-4f92-9503-a9545a252142/mutations.txt\n\nINFO     /tmp/biobb/unitests_167/pmxmutate/pmxmutate_log.out:cmd_wrapper.py:50 Exit code 0\n\nINFO     /tmp/biobb/unitests_167/pmxmutate/pmxmutate_log.out:cmd_wrapper.py:52 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_167/pmxmutate/pmxmutate_log.out:file_utils.py:391 Removed: [&amp;#x27;/tmp/biobb/unitests_167/pmxmutate/sandbox_30f44023-b099-411f-b053-a691e743ff28&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_167\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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