VMD-L Mailing List

From: Christopher Neale (chris.neale_at_mail.utoronto.ca)
Date: Fri Jun 28 2013 - 21:26:40 CDT

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.

Thank you,
Chris.