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

Dallas Warren Dallas.Warren at monash.edu
Tue Nov 15 02:13:41 CET 2011


Wont the volume be a function of the probe radius that is used?  And hence, if it is too big to fit through the ring, the volume will be larger than if the chain was straight?

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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