From: Axel Kohlmeyer (
Date: Wed Oct 25 2006 - 06:19:41 CDT

On Wed, 25 Oct 2006, Qiao Baofu wrote:

QB> Hi All
QB> I meet a problem in using vmd: I have a 980-molecules system obtained from
QB> Gromacs. But from the display VMD, there are some unexpected H-H bonds
QB> formation. Someone suggested that it is possible because of default
QB> bond-recognization of VMD. Thus I must provide the toplogy file to VMD to
QB> verify it. From the website of VMD, I found top2psf.tcl. After using it, I
QB> found that only one molecule's toplogy can be transfered. So the problem
QB> comes: when I use the one-molecules .psf and 980-molecules .pdb file (mol
QB> load psf md.pdf pdb md.pdb ), VMD complains "incorrect number of atoms". How
QB> to solve it?

as far as i can tell, you have three (or four?) options:

- change the unusual bonds manually and then write out an (incomplete)
 .psf file for future use with this system.
- change the top2psf script to be able to handle your system better
  (i would assume your setup was not expected by the author of the script)
- add a .tpr file reader to the molfile library.
- user a different program (but that is not really and option, right?).


QB> Thanks in advances.
QB> Sincerely yours,
QB> Baofu Qiao, PhD

Axel Kohlmeyer
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
If you make something idiot-proof, the universe creates a better idiot.