Re: previous question about multiplicity

From: Jim Phillips (
Date: Wed Jan 28 2004 - 14:12:45 CST


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.


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