Re: psfgen and bond topology specification

From: L. Michel Espinoza-Fonseca (
Date: Thu Mar 15 2007 - 16:53:03 CDT


As far as I know, psfgen is not that "smart". Based on my own experience,
most probably psfgen will be confused by the duplicated information that is
reading from your topology file.

One more thing: I always recommend people (including myself :)) to carefully
check a topology file created in their own before it is used. Even if psfgen
doesn't realize that something is not right, your simulations could be
potentially wrong. At the end, you'll have to walk the same path twice :)


2007/3/15, Neelanjana Sengupta <>:
> 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?
> Thanks,
> --
> ****************************************
> Neelanjana Sengupta, PhD student
> Dept. of Chemistry
> Univ. of California-Irvine
> Irvine, CA 92697
> Phone: 1-949-824 9921
> email:
> ****************************************

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