Does NAMD read the PDB element field?

From: Albrecht Goez (
Date: Fri Feb 01 2013 - 02:52:15 CST

Hi everyone,

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
Phone: +49 251 83 33289

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