VMD-L Mailing List

From: Magnus Andersson (magnus_at_helium.biomol.uci.edu)
Date: Wed Jun 15 2011 - 10:01:55 CDT

Check your topology file, for TIP3 it reads something like:

RESI TIP3 0.000 ! tip3p water model, generate using noangle nodihedral
GROUP
ATOM OH2 OT -0.834
ATOM H1 HT 0.417
ATOM H2 HT 0.417
BOND OH2 H1 OH2 H2 H1 H2 ! the last bond is needed for shake
ANGLE H1 OH2 H2 ! required
ACCEPTOR OH2
PATCHING FIRS NONE LAST NONE

You need to get rid of the last 2 entries in BOND, i.e.

 BOND OH2 H1 OH2 H2 ! H1 H2 ! the last bond is needed for shake

That should do it.

Cheers

/Magnus

===================================
Magnus Andersson, PhD
Department of Physiology and Biophysics
University of California, Irvine
Irvine, CA 92697-4560
(949) 824-6993
Fax: (949) 824-8540
===================================

On Jun 14, 2011, at 10:25 PM, PAUL NEWMAN wrote:

> Dear VMD Users
>
> Sorry I just realize that in my last email there is a typo.
> I have a problem when building my psf file. The water is forming bonds between hydrogens. In other words, what I did is that I mutated some animo acids in my protein (from an equilibrated simulation: protein + water + ions) and separated the protein from the water and ions in different pdb, since mutator does not support disulfide patch for proteins. I combine them using the following script (my pdbs and generating the new psf files) and I found that the hydrogens in the water are forming bonds between them. I also checked that in the original psf files there are less bond that in the new one. I believe I am doing something wrong. Can anyone give me a hand? Thanks
>
> ##############################
> package require psfgen
> topology top_all27_prot_lipid.inp
>
> alias residue HOH TIP3
>
> segment A { pdb protein.pdb }
> segment ION { pdb ions.pdb }
> segment SOLV { pdb water.pdb}
>
> patch DISU A:19 A:117
> patch DISU A:90 A:109
>
> coordpdb protein.pdb A
> coordpdb ions.pdb ION
> coordpdb water.pdb SOLV
>
> guesscoord
>
> writepsf new.psf
> writepdb new.pdb
>
> ##############################
>
>
>