checking for correct construction of dihedrals, etc.

From: Ralph Jimenez (
Date: Mon Dec 19 2005 - 16:51:52 CST

Hi everyone:

  My heme, even in solvent, is very nonplanar. It has some angles that
are extremely distorted compared to the reference structure. The
CHARMM27 topology and parameter files specify angles and impropers that
should constrain the conformation to near-planarity. I suspect that
NAMD may not be using these parameters.

  Is there a way to check if NAMD is using the dihedrals, angles, etc.?
I notice the log file lists the number of bonds, angles, dihedrals, but
can I get a specific list somehow to make sure the ones in the
simulation match the ones in the parameter/topology file?
  Best wishes,

Ralph Jimenez, Ph.D.
JILA and Department of Chemistry
440 UCB
University of Colorado, Boulder
Boulder, CO 80309-0440
Tel: (303) 492-8439
FAX: (303) 492-5235

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