From: Ralph Jimenez (rjimenez_at_jila.colorado.edu)
Date: Mon Dec 19 2005 - 16:51:52 CST
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?
-- 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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