VMD-L Mailing List

From: Brian Bennion (brian_at_youkai.llnl.gov)
Date: Fri Jul 02 2004 - 18:01:58 CDT

Hi Travis,

Last I heard from John, this feature will be in vmd 1.8.3 although a
current CVS snapshot from the vmd website may have the enhanced plugin.

For psf files do a search on the vmd and namd websites. A lot should pop
up including the program called psfgen which creates psf and pdb files
from other pdb files and the charmm topology libraries.

Regards
Brian

On Fri, 2 Jul 2004, Travis DePuy wrote:

> Hi all!
>
> I found this posting from last Oct.:
> www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/2005.html
>
> it mentions that there were plans to
> impliment CONECT in the pdb reader in
> VMD 1.8.2. Did it make it in? if so
> any ideas why I can't seem to get it
> to work? It is simply:
> 1 2
> 12345678901234567890
> CONECT 2345 345
> Yes?
>
> Is there anyother way to explicitly make
> bonds?
> I have seen tidbits about psf files, but
> where can I find the format/language desc
> info?
>
> Thanks much
> Travis
>

*****************************************************************
**Brian Bennion, Ph.D. **
**Computational and Systems Biology Division **
**Biology and Biotechnology Research Program **
**Lawrence Livermore National Laboratory **
**P.O. Box 808, L-448 bennion1_at_llnl.gov **
**7000 East Avenue phone: (925) 422-5722 **
**Livermore, CA 94550 fax: (925) 424-6605 **
*****************************************************************