VMD-L Mailing List

From: li (zlee_at_ustc.edu)
Date: Fri Mar 26 2004 - 01:00:28 CST

Replyed From: li <zlee_at_ustc.edu>
the lipid is DMPC,and the top file is top_all27_lipid.inp ,so guesscoord num is zero.the output info is all right,all the lipid molecules are the same ,so it is very strange only one lipid molecule has long bonds.
> 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:
> > &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; i have been using PSFGEN for a long time ,but recently ,when i used the lipid bilayer psf file it produced, NAMD encountered &nbsp;"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&nbsp;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 **
> **P.O. Box 808, L-448 bennion1_at_llnl.gov **
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