VMD-L Mailing List

From: Brian Bennion (brian_at_youkai.llnl.gov)
Date: Fri Oct 08 2004 - 21:58:07 CDT

Hi Matt

First you can't alias the URA to URA2, if URA is already a known residue
in the topology file.
If that is what you are actually doing?
The memory error is caused by psfgen/vmd, most likely because of the
previous comment.

Can you give some more information?
OS?
vmd version?
psfgen version? compiled or downloaded with vmd

Any other apps running at the same time?

Regards
Brian

On Fri, 8 Oct 2004, mdcooper wrote:

> I am trying to build a psf file for a complex with URA, except it is a URA
> molecule with an extra oxygen than the one provided in CHARMm so I have built
> URA2.
>
> I am aliasing URA to URA2 in the .pgn file.
>
> WHen I try to run the .pgn file it gets as far as extracting the 238 residues
> and then, apparently, reference bad memory and fails (ie the failure occurs
> outside of VMD). This is the same thing that happens when I tried to build a
> psf file with a molecule that contained hydrogens.
>
> Can anyone help - it is driving me nutty.
>
> thanks,
>
> matt
>
> ATOM 1806 CG2 ILE A 237 75.765 42.905 46.179 1.00 54.08
> ATOM 1807 CD1 ILE A 237 75.871 42.087 42.450 1.00 53.68
> ATOM 1808 N1 URA A 238 62.024 57.956 28.031 1.00 14.18
> ATOM 1809 C2 URA A 238 61.074 57.866 29.056 1.00 15.27
>
>

*****************************************************************
**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 **
**7000 East Avenue phone: (925) 422-5722 **
**Livermore, CA 94550 fax: (925) 424-6605 **
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