VMD-L Mailing List

From: Brian Bennion (brian_at_youkai.llnl.gov)
Date: Thu Mar 25 2004 - 11:42:45 CST

Hello Li,

This question can also be sent to the NAMD list, which might be more
appropriate.

In any case, you need to double check the output from psfgen exspecially
if it had to "guess" coordinates for any atoms. Then look at which atoms
have the long bonds in vmd and see if they make any sense, are the bonds
really supposed to connect these two atoms?

I suspect not, and that a terminating patch or some thing has been left
off when the psf file was generated.

Regards,
Brian

On Thu, 25 Mar 2004, li wrote:

> dear all:
>       i have been using PSFGEN for a long time ,but recently ,when i used the lipid bilayer psf file it produced, NAMD encountered  "the Bad global exclusion count, possible error!" problem.so i checked the psf file.all the generation process is all right ,all the VMD molecular info are right, too. but i can see some very long bonds in just one lipid molecule when loading the pdb and psf file together(all right when only the pdb loaded).so there must be something wrong with the psf file,but where did the problem come ? how to solve it ?
> BTY, the version is VMD 1.82
> Thanks in advance. 

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**Brian Bennion, Ph.D.                                         **
**Computational and Systems Biology Division                   **
**Biology and Biotechnology Research Program                   **
**Lawrence Livermore National Laboratory                       **
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