Re: I need help with this

From: Richard Wood (
Date: Fri Feb 11 2011 - 12:00:11 CST

Chris, your suggestion implies that a) none of the residues have the same
"number" as other residues and b) there are not too many of each residue (i.e <
10000 waters, for example).

The problem I had was that I had 560 POPC residues and they were not numbered
from 1 to 560. They were numbered in blocks from 1 (up)to 30. So, when you
read them in, all the residues with the same number got overwritten.

Autopsf in VMD apparently ignores this.


From: Chris Harrison <>
To: Richard Wood <>
Sent: Fri, February 11, 2011 11:42:41 AM
Subject: Re: namd-l: I need help with this


Create a psf/pdb set for each seperate molecular
system (moleculeA.psf, moleculeA.pdb, moleculeB.psf, etc),
then in VMD use a script similar to the following:

package require psfgen

psfcontext reset

topology top_all22_prot.inp

readpsf moleculeA.psf
coordpdb moleculeA.pdb

readpsf moleculeB.psf
coordpdb moleculeB.pdb

writepsf myNewSystem.psf
writepdb myNewSystem.pdb


Chris Harrison, Ph.D.
Theoretical and Computational Biophysics Group
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801                          Voice: 217-244-1733              Fax:   217-244-6078
Richard Wood <> writes:
> Date: Wed, 9 Feb 2011 11:01:25 -0800 (PST)
> From: Richard Wood <>
> To:
> Subject: namd-l: I need help with this
> X-Mailer: YahooMailRC/555 YahooMailWebService/
> Hi all,
> I'm trying to set up a system where I have a lipid bilayer and I want to 
> "attach" a small molecule to the surface so I can run dynamics.
> I have generated the bilayer using VMD and I have built the small molecule and 
> have parameters and a topology for it.  The problem I am having is in 
> the psf for the total system.
> I have the *.pdb and *.psf for the bilayer and I can run that in namd; in fact, 
> I am minimizing it now as a test.  However, when I try to generate a psf file, 
> because the bilayer is numbered "funny", some residues have the same number and 
> don't get converted to the new file.  If I try to renumber everything by hand, 
> then it won't minimize (it gets to about 27 steps and then I get "weird 
> like -1.
> I'm wondering if anyone has encountered this before and what the workaround 
> TIA,
> Richard

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