From: Peter Freddolino (
Date: Mon Jun 15 2009 - 06:50:46 CDT

Hi Ruchi,m
the H-H bond is not an automatically added bond, but rather, is present
in your topology file. You need to remove it from the topology file if
you want to get rid of that bond.

Ruchi Sachdeva wrote:
> 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
> guesscoord
> writepdb protein.pdb
> writepsf protein.psf
> exit
> Please suggest how to avoid this?
> Thanks in advance
> Regards
> Ruchi