VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Sun Apr 30 2006 - 09:24:22 CDT

Hi,
  It depends. The PSF files written by VMD using atom selection
'$sel writepsf' are legal, but incomplete (no angles/dihedrals/impropers,
etc, presently anyway). In the case of the psfgen plugin, they are
written in X-PLOR format (uses names rather than absolute indices
for references to the top/par files). I don't know if Charmm is able
to load these directly, here was a previous discussion of this issue:
  http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/4802.html

If any Charmm experts know of a way to load the X-PLOR formatted PSF files
feel free to chime in.

  John Stone
  vmd_at_ks.uiuc.edu
  
On Sun, Apr 30, 2006 at 10:59:52AM +0100, mahmoud wrote:
> Hi
> Can any one tell me if psf file created by VMD is compatible with charmm
> (charmm can read it)and how can I make pdb/psf files can be read by charmm.
> any help would be appreciated
> thanks
>
> --On Saturday, April 29, 2006 10:48 PM -0500 John Stone <johns_at_ks.uiuc.edu>
> wrote:
>
> >
> >Hi,
> > VMD is compiled on Windows using the MSVC tools rather than
> >with straight makefiles. The win32 plugins are compiled using
> >makefiles however. Compiling VMD itself on Windows is actually
> >quite easy, but getting all of the other libraries built can be
> >a serious pain. Unless you're up to the daunting task of
> >compiling all of the libraries VMD needs with the right runtime
> >library linkage etc, I'd suggest building on one of the other
> >platforms if you're just modifying the code for your own
> >experiments.
> >
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> >On Sat, Apr 29, 2006 at 11:12:23PM -0400, Chang Hu wrote:
> >>Hi,
> >>
> >>A quick question: is there any way to build VMD in Windows? I saw a
> >>"WIN32" option in make_distribut but not in Makefile.
> >>
> >>Thanks,
> >>Chang
> >
> >--
> >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
>
>
>
> Mahmoud E. Soliman
> Department of chemistry (Computational chemistry& Modelling)
> University of Bath
> Bath
> BA2 7AY 

-- 
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