VMD-L Mailing List

From: Qiao Baofu (qiaobf_at_gmail.com)
Date: Wed Oct 25 2006 - 04:31:31 CDT

Hi All

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

Thanks in advances.

Sincerely yours,
Baofu Qiao, PhD