VMD-L Mailing List

From: campen_at_geosc.psu.edu
Date: Tue Jul 18 2006 - 08:32:37 CDT

Dear all:

I've been trying to use the builder and Amber parameter set available for
carbohydrates from Robert Woods group (www.glycam.com) and visualize these
structures in VMD (in preparation for simulating them in NAMD).

I've found that I can generally produce a structure for a small test case
(if I read in first the PARM information and then the .crd file) but most
of the geoemtric parameters are screwed up (e.g. one atom is about 30
angstroms away from the others).

Any suggestions as to how to solve this issue would be greatly appreciated.

Kramer Campen