From: Brian Bennion (brian_at_youkai.llnl.gov)
Date: Wed Jan 28 2004 - 14:18:20 CST
Psfgen indeed places a repeated dihedral. but I didn't think this was a
problem initially. Now I am not so sure.
The are three other dihedrals that are repeated in the psf file generated
by psfgen. ie CA CA CA HP and HP CA CA CA.
Maybe my topology file is causing problems???
Brian
On Wed, 28 Jan 2004, Jim Phillips wrote:
> Hi,
>
> Looking at the code myself, the only way you should see this error is if
> you have a repeated dihedral (i.e., same atom numbers) listed in the
> structure (psf) file. This might be because of a repeated dihedral in the
> topology file used to generate the structure. Unfortunately the actual
> atom numbers are not passed to the code that generates this error message.
> In any case, there are only a small number of atoms to examine in the psf
> file to check this. Let us know what you find.
>
> -Jim
>
>
> On Tue, 27 Jan 2004, Brian Bennion wrote:
>
> >
> > Hello,
> >
> > After looking through the code I think I know what is going
> > on.
> >
> > First, I declare my parameter type as charmm format. So
> > then namd assumes that psf file will only contain torsions that are
> > unique, within 1 atom.
> >
> > Since my ligand has two benzyl groups with the Carbons
> > assigned the CA type, namd reads the second benzyl group and thinks that
> > it is adding multiplicity and dies because it isn't in XPLOR mode.
> >
> > This, I think, is a bug in NAMD. NAMD needs another check to
> > show that the second group of CA CA CA CA is unique but doesn't represent
> > a new torsion parameter. It should use the one already loaded in.
> >
> > *****************************************************************
> > **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 **
> > *****************************************************************
> >
>
*****************************************************************
**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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