Hi
  I want to perform   peptide + popc membrane simulation. I download 
popc128a.pdb from
  (http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies).
  Before I introduce the peptide into the membrane, the water layer had to be 
broadened to ensure full solvation of the peptide .I increase the water layer 
using the following commands
  1. editconf  -f  popc128a.pdb  -o  po_box.pdb  -box  6.1065  6.1059  9.0000  
-c
  2. genbox  -cp  po_box.pdb  -cs  -o  po_sol.pdb  -p  lip.top
   
  Now, the no. of water molecules over the bilayer  increased . But, the 
problem is that  there are water molecules inside the bilayer, which were 
absent incase of popc128a.pdb. How can I remove these offending water molecules?

       
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