Re: Re: psfgen and CHARMM19 explicit exclusions

From: Andrey (
Date: Sat Sep 29 2012 - 13:04:37 CDT

Dear Chris,

I'm using psfgen to create PSF files for use with the software developed
by our group (it is not yet published, though we hope to release it in
this year).

I think that writing explicit exclusions to PSF might benefit other
users, since resulting files will be more conforming to standard (or at
least to what Xplor uses). Besides, in past there has been several
questions to this list regarding errors psfgen spat when parsing
topology files with explicit exclusions.

I haven't performed any elaborate testing of NAMD handling of explicit
exclusions, but it seemed to work fine.

I'll clean the code and submit the patch to, right?

With best regards,
Andrey Alekseenko
On 09/28/2012 10:24 PM, Chris Harrison wrote:
> Andrey,
> NAMD internally determines exclusions and thus does not need the explicit exclusion list in CHARMM format psf files.
> However, if you are using psfgen for some other software requiring the explicit exclusions, you can send the patch (off list) and we'll' review it for potential inclusion in psfgen. If this is the case, please also let us know what software package you are using.
> On the other hand, if you have tests that show NAMD is not handling exceptions for CHARMM19 in a proper manner, please let us know and send your tests with their results so we can look into this ASAP.
> Best,
> Chris
> Andrey <> writes:
>> Date: Thu, 27 Sep 2012 23:48:29 -0400
>> From: Andrey <>
>> To:
>> Subject: Re: namd-l: Re: psfgen and CHARMM19 explicit exclusions
>> User-Agent: Mozilla/5.0 (X11; Linux x86_64; rv:15.0) Gecko/20120827
>>   Thunderbird/15.0
>> If this list is not the best place to ask such questions, please
>> direct me to the right place.
>> I really want to know what is the best way to distribute version to
>> psfgen, patched for use with particular piece of software?
>> The modifications are minimal.
>> Should I include just the patch file and link to UIUC site, or can I
>> distribute the complete patched source?
>> -- 
>> Thanks in advance,
>> Andrey Alekseenko
>> <>
>> On 09/17/2012 11:38 PM, Andrey wrote:
>>> 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 definitions.
>>> 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.
> Best,
> Chris
> --
> Chris Harrison, Ph.D.
> NIH Center for Macromolecular Modeling and Bioinformatics
> Theoretical and Computational Biophysics Group
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801
>       Voice: 773-570-6078
>               Fax:   217-244-6078

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