From: John Stone (
Date: Fri Oct 27 2006 - 13:21:31 CDT

  The H-H bonding problem you describe was likely caused by a small bug in
the bond search code of VMD 1.8.4 and 1.8.5 that caused the H-H bond culling
code to be ineffectual. This has been fixed in the test versions of
VMD 1.8.6, and I've got a new test version posted if you'd like to try
it out:

Let me know if you need more help with this.

  John Stone

On Wed, Oct 25, 2006 at 11:31:31AM +0200, Qiao Baofu wrote:
> 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

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