VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Fri Jun 28 2013 - 22:23:31 CDT

On Sat, Jun 29, 2013 at 4:26 AM, Christopher Neale
<chris.neale_at_mail.utoronto.ca> wrote:
> Dear VMD users:
>
> I have coordinates and Desmond parameters for a molecule and would like to create input files for Desmond. One of the initial steps in doing so is to create a DMS file. The Desmond User Manual suggests loading a .psf and .pdb into vmd, then exporting coordinates as a DMS file. The problem is that I do not have a .psf file, nor do I have parameters in a format that can be used by psfgen. I have tried loading the .pdb into VMD and saving it as a .dms file, but when I then reload that .dms file into VMD, it is clear that the bond information (correctly determined by VMD from a distance search upon loading in the .pdb file) is not saved to the .dms file.
>
> Does anybody know how to get the bonds that are displayed by VMD to be written to the .dms file? I presume that there is some way to do this using the TK console if I have a list of bonds.

you usually need more than just the bonds. the psf file contains
masses, charges, atom types, bond, angle, dihedrals, etc.
it does not contain the force field parameters. the following shows
how to set this up for LAMMPS, but the difference is simply the final
write command. so have a look and see, if it can work for you.
https://sites.google.com/site/akohlmey/software/topotools/topotools-tutorial---introduction

axel.

> Thank you,
> Chris.
>
>
> 

--
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
International Centre for Theoretical Physics, Trieste. Italy.