Refs #1 Find closest water to protein

confinedBSA.ipynb

@@ -1,7 +1,7 @@
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@@ -185,7 +185,19 @@
       "- <code>Select group for centering: Group     1 (        Protein) has  9173 elements</code>  \n",
       "- <code>Select group for output: Group     0 (         System) has 84738 elements</code>  \n",
       "Produces file <code>relax_2_centered.gro</code>.  \n",
-      "<center><a href=\"files/simulation/monomer/solvatedBSA/minimize/relax/relax_2_centered.gif\"><img src=\"files/simulation/monomer/solvatedBSA/minimize/relax/relax_2_centered.gif\" width=\"200\"></a>  [relax_2_centered.gif](files/simulation/monomer/solvatedBSA/minimize/relax/relax_2_centered.gif)</center>"
+      "<center><a href=\"files/simulation/monomer/solvatedBSA/minimize/relax/relax_2_centered.gif\"><img src=\"files/simulation/monomer/solvatedBSA/minimize/relax/relax_2_centered.gif\" width=\"200\"></a>  [relax_2_centered.gif](files/simulation/monomer/solvatedBSA/minimize/relax/relax_2_centered.gif)</center>\n",
+      "\n",
+      "<b>Select closest N water molecules to protein</b>:  \n",
+      "Save the following selection to file <i>selection_close_waters.txt</i>:\n",
+      "\n",
+      "<code>close_solvent_atoms = group \"SOL\" and within 0.5 of group \"Protein\";\n",
+      "close_solvent_molecules = same resindex as close_solvent_atoms;\n",
+      "stripped_system = group \"Protein\" or close_solvent_molecules;</code>\n",
+      "\n",
+      "Create index file <i>stripped_system.ndx</i> with protein plus close waters, and also PDB file [stripped_system.pdb](files/simulation/monomer/solvatedBSA/minimize/relax/stripped_system.pdb)\n",
+      "gmx select -f relax_2_centered.gro -s relax_2_centered.gro -sf selection_close_waters.txt -on stripped_system.ndx -ofpdb junk.pdb -pdbatoms selected\n",
+      "\n",
+      "<center><a href=\"files/simulation/monomer/solvatedBSA/minimize/relax/stripped_system.png\"><img src=\"files/simulation/monomer/solvatedBSA/minimize/relax/stripped_system.png\" width=\"200\"></a></center>"
      ]
     },
     {