From: Javier Goicochea (goicox_at_gmail.com)
Date: Mon Feb 02 2009 - 08:33:15 CST

Hi All,

Could it be possible to read the BOND connectivity from a PSF file and
create ANGLES and DIHEDRALS automatically in VMD? I would like to compare my
results with VMD.

Regards, Javier

On Fri, Jan 16, 2009 at 4:31 PM, John Stone <johns_at_ks.uiuc.edu> wrote:

>
> Hi,
> You want to read the source code for psfgen, as that's where the
> generation of bonds, angles, dihedrals, etc is done. It's found in
> the plugin tree, in plugins/psfgen/src
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Fri, Jan 16, 2009 at 09:17:00AM +0100, Javier Goicochea wrote:
> > Hi All,
> >
> > By executing psfgen or writepsf angles and dihedrals can be automatically
> > created in PSF files. Since these are created quite fast in VMD, I would
> > like to have a similar implemetation in my code. I need to create
> suitable
> > PSF files for crystalline structures and fluids in complex geometries
> > arrangements.
> >
> > Can somebody tell me where is the location of code that perform these
> tasks
> > in VMD? Which files, functions, objects, and headers are involved?
> >
> > Thank you in advance, Javier
>
> --
> 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/ <http://www.ks.uiuc.edu/%7Ejohns/>
> Fax: 217-244-6078
>