From: Ruchi Sachdeva (
Date: Mon Jun 15 2009 - 03:57:25 CDT

Dear All,

I am trying to create psf file for my system using psfgen. Despite using
auto none for building the water segment, H-H bonds are still being made. I
have tested for other systems, the same thing is happening there also. I am
using VMD-1.8.6. Following is the psfgen script:

package require psfgen
topology ~/toppar/top_all27_prot_lipid.rtf
pdbalias residue HIS HSE
pdbalias atom ILE CD1 CD
segment U {pdb chaina.pdb}
coordpdb chaina.pdb U
pdbalias atom HOH O OH2
pdbalias residue HOH TIP3
segment WC {
auto none
pdb wat.pdb
coordpdb wat.pdb WC
writepdb protein.pdb
writepsf protein.psf

Please suggest how to avoid this?

Thanks in advance