previous question about multiplicity

From: Brian Bennion (
Date: Tue Jan 27 2004 - 19:06:02 CST


After looking through the code I think I know what is going

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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