Re: I need help with this

From: Chris Harrison (charris5_at_gmail.com)
Date: Fri Feb 11 2011 - 12:44:42 CST

Perhaps I did not. :) Perhaps it could be explained more clearly, if
you still require our assistance.

Richard Wood <rwoodphd_at_yahoo.com> writes:
> Date: Fri, 11 Feb 2011 10:39:57 -0800 (PST)
> From: Richard Wood <rwoodphd_at_yahoo.com>
> To: Chris Harrison <charris5_at_gmail.com>
> Cc: namd-l_at_ks.uiuc.edu
> Subject: Re: namd-l: I need help with this
> X-Mailer: YahooMailRC/555 YahooMailWebService/0.8.109.292656
>
> I don't think you understand the problem. :)
>
> 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 12:08:56 PM
> Subject: Re: namd-l: I need help with this
>
> 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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