VMD-L Mailing List

From: Edward Lyman (edward.lyman_at_gmail.com)
Date: Fri Apr 29 2011 - 14:30:53 CDT

Thanks for the reply. Now I have used vmd 1.9 to delete a single cholesterol
by

(1) read in psf and pdb for the full system
(2) define an atom selection that excludes the problematic cholesterol:
> set write_sel [atomselect top "not same fragment as index foo"]
(3) renumber residues
> $write_sel set resid [$write_sel get residue]
(4) write psf/pdb
> $write_sel writepsf new.psf
> $write_sel writepdb new.pdb

This writes a psf that looks ok through the bonds section, but the angles,
dihedrals, impropers have problems. There are the same number of angles in
the new as in the original psf. (Theres hould be fewer because there is one
less chol) And, the angles include triplets like "1 2 2 " in the first 50 or
so lines, then the angle lines are all "1 1 1 1 1 1 1 1 ". same for
dihedrals, etc.

So, am I missing an autogenerate statement? It seems possible that
autogenerate may not get the angles, dihedrals etc correct...is that a real
concern?

Thanks,
Ed

On Fri, Apr 29, 2011 at 9:40 AM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:

> On Fri, Apr 29, 2011 at 9:00 AM, Edward Lyman <edward.lyman_at_gmail.com>
> wrote:
> > Thanks for the work around, it's very much appreciated. But, it occurs to
> me
> > now...why can't I simply use $sel writepsf blah.psf and $sel writepdb
> > blah.pdb from the vmd console to write out a psf and a pdb for selections
> > which delete the unwanted molecules? ie, why bother with psfgen at all
> when
> > you already have in hand a psf that contains all the correct force field
> > terms, etc, and you just want to delete a few molecules?
>
> you can do this. the functionality to store and write out the complete
> topology
> information from and to .psf files has not been around that long and before
> that
> using psfgen was the only option. not everybody is aware of this new
> functionality
> in VMD and various plugins and scripts are only slowly being migrated to
> make
> use of these new features (why break something that works?).
>
> cheers,
> axel.
>
> >
> > Thx,
> > Ed
> >
> >
> >
> >
> > On Tue, Apr 26, 2011 at 3:21 PM, Jim Phillips <jim_at_ks.uiuc.edu> wrote:
> >>
> >> If you can't get CHARMM-GUI to write a non-EXT, non-CHEQ format PSF (I
> >> don't think you need either of those options) then try reading the file
> into
> >> VMD, writing it out again, and using that file with psfgen.
> >>
> >> If you use the psfgen binary from NAMD 2.8b1 you can probably read the
> >> file with "readmol psf 50_50_10nm.xplor.psf" since that uses the VMD
> plugins
> >> (I don't think VMD's psfgen module has plugins enabled yet).
> >>
> >> -Jim
> >>
> >>
> >> On Tue, 26 Apr 2011, Edward Lyman wrote:
> >>
> >>> attached is the psf.
> >>>
> >>> Any suggestions for a workaround? I want to delete a couple lipid
> >>> molecules
> >>> as described in the psfgen docs...if there is some othe way to
> accomplish
> >>> this, I am all ears.
> >>>
> >>> E
> >>>
> >>>
> >>> On Tue, Apr 26, 2011 at 11:53 AM, John Stone <johns_at_ks.uiuc.edu>
> wrote:
> >>>
> >>>> Hi,
> >>>> It seems that psfgen doesn't like the X-PLOR format PSF file you've
> >>>> got,
> >>>> although the VMD PSF plugin seems to read it without trouble.
> >>>>
> >>>> Can you send me a gzipped copy of the PSF file that is causing you
> >>>> trouble?
> >>>>
> >>>> This is most likely a limitation of the PSF reader currently in
> psfgen,
> >>>> and is something we are looking at improving.
> >>>>
> >>>> Cheers,
> >>>> John Stone
> >>>> vmd_at_ks.uiuc.edu
> >>>>
> >>>> On Fri, Apr 22, 2011 at 11:03:30AM -0400, Edward Lyman wrote:
> >>>>>
> >>>>> Hi all,
> >>>>>
> >>>>> I am trying to use psfgen to delete a couple of lipids and write a
> >>>>> new
> >>>>> psf/pdb pair. The toplogy files read in fine, but when I read teh
> >>>>> psf,
> >>>>
> >>>> I
> >>>>>
> >>>>> get:
> >>>>>
> >>>>> reading structure from psf file 50_50_10nm.xplor.psf
> >>>>> Error processing bonds
> >>>>>
> >>>>> MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over.
> >>>>> psfplugin) Detected a Charmm31 PSF file
> >>>>> psfplugin) Detected a Charmm31 PSF EXTEnded file
> >>>>> Info) Using plugin psf for structure file 50_50_10nm.xplor.psf
> >>>>> psfplugin) no cross-terms defined in PSF file.
> >>>>> Info) Analyzing structure ...
> >>>>>
> >>>>> I am running vmd 1.9, psfgen 1.5. The psf file is an xplor psf
> (runs
> >>>>
> >>>> in
> >>>>>
> >>>>> namd) that was written by the charmm gui. The psf/pdb pair work
> just
> >>>>
> >>>> fine
> >>>>>
> >>>>> for reading into vmd.
> >>>>>
> >>>>> Any help is appreciated.
> >>>>> Ed
> >>>>
> >>>> --
> >>>> NIH Resource for Macromolecular Modeling and Bioinformatics
> >>>> Beckman Institute for Advanced Science and Technology
> >>>> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> >>>> http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> >>>> http://www.ks.uiuc.edu/Research/vmd/ Fax: 217-244-6078
> >>>>
> >>>
> >
> >
>
>
>
> --
> Dr. Axel Kohlmeyer
> akohlmey_at_gmail.com http://goo.gl/1wk0
>
> Institute for Computational Molecular Science
> Temple University, Philadelphia PA, USA.
>