psfgen and CHARMM19 explicit exclusions

From: Andrey (
Date: Tue Sep 11 2012 - 21:10:20 CDT

Dear all,

Currently (NAMD 2.9), psfgen utility does not support explicit
exclusions in CHARMM19 forcefield, although they are essential part of
said forcefield.

For personal use I've implemented the handling of explicit exclusions
into psfgen utility. Currently "support" is limited to producing correct
(i.e. '!NNB' section in .psf produced by psfgen does not differ from
.psf produced by CHARMM) .psf file from .pdb and CHARMM topology.

I would like to know if it could be included in the official release.
If so, I can add support for reading in exclusion lists from .psf's,
perform better testing and submit a patch.

With best regards,
Andrey Alekseenko

This archive was generated by hypermail 2.1.6 : Mon Dec 31 2012 - 23:22:04 CST