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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