[gmx-users] molecular surface area(MSA)?

Dallas Warren Dallas.Warren at monash.edu
Fri Oct 22 00:29:24 CEST 2010

What you want then is a Connolly surface?


Which I gather is what GROMACS actually calculates,


Catch ya,

Dr. Dallas Warren

Medicinal Chemistry and Drug Action

Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at monash.edu

+61 3 9903 9304
When the only tool you own is a hammer, every problem begins to resemble
a nail. 


From: gmx-users-bounces at gromacs.org
[mailto:gmx-users-bounces at gromacs.org] On Behalf Of jagannath mondal
Sent: Friday, 22 October 2010 9:19 AM
To: gmx-users at gromacs.org
Subject: [gmx-users] molecular surface area(MSA)?



  I was wondering whether gromacs can calculate a quantity called
molecular surface area(MSA) which is different from solvent accessible
surface area(SASA).


By definition, SASA of a molecule is the area of surface traced by
center of a spherical water probe rolling on a vander wall surface of
the given molecule. I think g_sas provides SASA.


But MSA is something different. It is the area generated by the part of
the probe surface facing the given molecule. But, I am not sure whether
gromacs can calculate it .




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