Perhaps the radius of gyration could also be used! Ptraj calculates that directly.
John Cannon
Genetics Program Chair and
Associate Professor of
Molecular Microbiology and Immunology
University of Missouri
1 Hospital Drive
Columbia, Missouri 65212
-----Original Message-----
From: Brian Radak [mailto:radak004.umn.edu]
Sent: Tuesday, February 28, 2012 8:24 AM
To: AMBER Mailing List
Subject: Re: [AMBER] Calculate the volume of a protein from the trajectory
Do you mean like an excluded volume? Something like that might be able to be calculated from a solvent radial distribution function (the "radial"
command in ptraj). That might be tricky and also not what you mean/want.
Regards,
Brian
On Tue, Feb 28, 2012 at 2:41 AM, surasak chunsrivirot <fa833.hotmail.com>wrote:
>
> Dear all,
>
> I'm wondering if there is a command in AMBER to calculate the volume
> of a protein from the trajectory. Specifically, I want to calculate
> the average volume of the protein from the last 10 ns trajectory. Any
> suggestions on this issue would be greatly appreciated.
>
> Thank you very much for your help,
> Surasak
>
>
>
>
>
>
>
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--
================================ Current Address =======================
Brian Radak : BioMaPS
Institute for Quantitative Biology
PhD candidate - York Research Group : Rutgers, The State
University of New Jersey
University of Minnesota - Twin Cities : Center for Integrative
Proteomics Room 308
Graduate Program in Chemical Physics : 174 Frelinghuysen Road,
Department of Chemistry : Piscataway, NJ
08854-8066
radak004.umn.edu :
radakb.biomaps.rutgers.edu
====================================================================
Sorry for the multiple e-mail addresses, just use the institute appropriate address.
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Received on Tue Feb 28 2012 - 07:00:02 PST
