VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri May 05 2006 - 10:00:11 CDT

Marc,
  The mail you saw below was a question about psfgen rather than about
the $sel write function in VMD, which are two different things. What
Justin wrote is correct in terms of writing PSF files with psfgen.
Your question asked about writing them from VMD atom selections,
which is a different story. The source of confusion is likely that
the VMD atom selection and psfgen "writepsf" commands are confusingly
similar so it's easy to mistake the two.

  John Stone
  vmd_at_ks.uiuc.edu

On Fri, May 05, 2006 at 03:50:23PM +0100, MW Van der Kamp, School of Chemistry wrote:
> Hi John,
>
> I'm running version 1.8.3 on the moment.
> But I gather from your reaction that CHARMM psf files can't be written yet.
> I got my hopes up after finding the following post in the VMD-l archive:
>
> ***************
> On Dec 3, 2003, at 10:05 PM, Mike McCallum wrote:
>
>
> >
> >I seem to remember asking this question before, but I can't seem to
> >find any answer, so here goes:
> >
> >Using psfgen through vmd and tkcon is really a great thing, but what
> >if you want to use the psf file in charmm? Charmm will *write* XPLOR
> >format psf, but not read. Will psfgen generate charmm-type psf files?
> >I'm almost sure that it can, but I can't find it in the docum
>
>
> Yes:
>
>
> writepsf charmm foo.psf
>
>
> will write in charmm format. "writepsf x-plor foo.psf" will write in
> x-plor format, as will "writepsf foo.psf".
>
> Cheers,
> Justin
> ******************
>
> Thanks for your reaction, and I hope writing charmm psf-files will be added
> as a feature in a next version of VMD.. ;)
>
> Marc
>
>
>
> --On 05 May 2006 09:42 -0500 John Stone <johns_at_ks.uiuc.edu> wrote:
>
> >
> >Marc,
> > Which version of VMD are you running? ('vmdinfo version' will tell you
> >if it's not clear)
> >The PSF files written by VMD atom selections (in the current version)
> >will lack angles, dihedrals, impropers, and cross-terms. Also, there's
> >no "charmm" keyword currently. The right syntax is:
> > set sel [atomselect top all]
> > $sel writepsf test.psf
> >
> >Thanks,
> > John stone
> > vmd_at_ks.uiuc.edu
> >
> >On Fri, May 05, 2006 at 03:02:37PM +0100, MW Van der Kamp, School of
> >Chemistry wrote:
> >>Hi,
> >>
> >>> From what I thought and previous posts, one should be able to write a
> >>psf-file in CHARMM format by making a selection of all atoms ('set all
> >>[atomselect top all]') and then use the following:
> >>
> >>$all writepsf charmm test.psf
> >>
> >>When I try this however, I get 'atomselection: improper method:
> >>writepsf'... What am I doing wrong?
> >>
> >>Thanks in advance for any help,
> >>Marc
> >>
> >>---------------------------------------------------
> >>Marc van der Kamp, PhD-student
> >>School of Chemistry, Research group of Dr. Adrian Mulholland
> >>University of Bristol
> >>E-mail: Marc.vanderKamp_at_bristol.ac.uk
> >>
> >
> >--
> >NIH Resource for Macromolecular Modeling and Bioinformatics
> >Beckman Institute for Advanced Science and Technology
> >University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> >Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> > WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
>
>
>
> ---------------------------------------------------
> Marc van der Kamp, PhD-student
> School of Chemistry, Research group of Dr. Adrian Mulholland
> University of Bristol
> E-mail: Marc.vanderKamp_at_bristol.ac.uk
> 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078