From: Albrecht Goez (a.goez_at_uni-muenster.de)
Date: Fri Feb 01 2013 - 02:52:15 CST
Does anyone know whether NAMD makes use of the element field in the
input PDB file? Because of a faulty topology file, some oxygens in my
system were marked as carbons in this column. However, the atom type as
well as the mass were set correctly. The topology entry looked like this:
MASS 26 OK 15.99940 C ! ketone oxygen
and in the residue definiton (for example)
ATOM OBB OK -0.56500
So it's really just the entry in the last PDB column that was wrong.
Will that affect the simulation?
Best regards, Albrecht
-- M.Sc. Albrecht Goez Theoretische Organische Chemie Organisch-Chemisches Institut Westfälische Wilhelms-Universität Münster Corrensstraße 40 48149 Münster Germany Phone: +49 251 83 33289 Email: a.goez_at_uni-muenster.de
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