psfgen and bond topology specification

From: Neelanjana Sengupta (
Date: Thu Mar 15 2007 - 16:20:24 CDT

Hi NAMD users,

I generally use psfgen to create my .psf files to run with NAMD. I have
simulated some unnatural amino acid chains, for which I had to modify the
CHARMM topology files. Now, my question is this:
If in a topology, in the 'BOND' section, a certain bond is specified more
than once (accidentally, say), would psfgen be able to detect that? In other
words, how will psfgen deal with a will an 'error' such as,

BOND CA1 O1 CA1 CA2 CA2 O2 N1 H1 CA1 O1

(the CA1 O1 bond is specified twice).
Is psfgen smart enough to override this and create the correct .psf files?


Neelanjana Sengupta, PhD student
Dept. of Chemistry
Univ. of California-Irvine
Irvine, CA 92697
Phone: 1-949-824 9921

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