[gmx-users] RE: Questionable van der waals volumes from g_sas

Dallas Warren Dallas.Warren at monash.edu
Tue Nov 15 02:15:17 CET 2011

Sorry, ignore my last post, only just realised you had set your probe to 0 radius.

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 Jacob Alan Spooner
Sent: Tuesday, 15 November 2011 11:29 AM
To: gmx-users at gromacs.org
Subject: [gmx-users] Questionable van der waals volumes from g_sas

Hello gmx-users

I have been attempting to obtain van der Waal's volumes using the g_sas utility.  The command I use to do so is something like

g_sas -f hexane.gro -s topol.tpr -probe 0 -tv V_vdw.xvg

This seems to give reasonable results for most of my test systems, however when I run the command on an optimized structure of cyclohexane I get a larger van der Waal's volume than that of n-hexane.  I think this has to do with the fact that the surface calculation method used in g_sas is missing the void in the centre of the ring.  In order to test this I increased the size of the ring, calculating the volumes of icosane and cycloicosane.  I found that in this case the volume of the cyclic molecule was expectedly smaller.  I tried increasing the number of dots used to draw the dot-surface but saw no significant change in the volumes.

Therefore my question is if anybody is familiar enough with g_sas to help me understand why the surface calculation method is not giving sensible values for these smaller ring systems.  Also I am wondering if anybody can suggest any other free software that would allow me to compute van der Waal's and Solvent Excluded volumes.

Thanks in advance.

Jake Spooner
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