Re: I need help with this

From: Chris Harrison (charris5_at_gmail.com)
Date: Fri Feb 11 2011 - 12:08:56 CST

Richard Wood <rwoodphd_at_yahoo.com> writes:
> 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).

Almost, but not exactly. It implies that no resid have no more than
one atom with the same index, and that no segname have more than one
residue with the same resid. This is a requirement of psfs in general
for namd.

> 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.

Use 30 different segnames.

>
> Richard
>
>
>
>
>
> ________________________________
> From: Chris Harrison <charris5_at_gmail.com>
> To: Richard Wood <rwoodphd_at_yahoo.com>
> Cc: namd-l_at_ks.uiuc.edu
> Sent: Fri, February 11, 2011 11:42:41 AM
> Subject: Re: namd-l: I need help with this
>
> Richard,
>
> 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
> resetpsf
>
> topology top_all22_prot.inp
>
> readpsf moleculeA.psf
> coordpdb moleculeA.pdb
>
> readpsf moleculeB.psf
> coordpdb moleculeB.pdb
>
> writepsf myNewSystem.psf
> writepdb myNewSystem.pdb
>
>
>
> Best,
> Chris
>
>
> --
> 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
>
> char_at_ks.uiuc.edu Voice: 217-244-1733
> http://www.ks.uiuc.edu/~char Fax: 217-244-6078
>
>
> Richard Wood <rwoodphd_at_yahoo.com> writes:
> > Date: Wed, 9 Feb 2011 11:01:25 -0800 (PST)
> > From: Richard Wood <rwoodphd_at_yahoo.com>
> > To: namd-l_at_ks.uiuc.edu
> > Subject: namd-l: I need help with this
> > X-Mailer: YahooMailRC/555 YahooMailWebService/0.8.108.291010
> >
> > 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
> >generating
> >
> > 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
> >numbers"
> >
> > like -1.
> >
> > I'm wondering if anyone has encountered this before and what the workaround
> is.
> >
> > TIA,
> > Richard
> >
> >
> >
> >
>
>
>
>

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