Re: psfgen and CHARMM19 explicit exclusions

From: Andrey (
Date: Mon Sep 17 2012 - 22:38:24 CDT

Okay, no one seems interested in this.

Then I have the following question:

Is such patched version considered a "derivative work", or is it still
considered the same software? The license agreement is not clear on

What is the best way to include modified 'psfgen' as part of our own
software distribution? The modifications include stripping away
everything besides 'psfgen/' directory, making changes to psfgen source
code for correct handling of CHARMM19 explicit exclusions and writing
custom Makefile.

With best regards,
Andrey Alekseenko
On 09/11/2012 10:10 PM, Andrey wrote:
> 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
> <>

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