Re: AMBER: molsurf error in MM/PBSA calculation

From: David A. Case <>
Date: Tue, 12 Jul 2005 18:23:50 -0700

On Wed, Jul 13, 2005, JunJun Liu wrote:
> Thank you for response! Attached please find the gzipped pqr file. The
> command I executed and the corresponding output are as follows:
> ---------
> $ molsurf test.pqr 0.0
> 5069 atoms read
> odd number of probe positions on torus!
> ---------
> Please help me resolve this problem, thanks in advance!

I have no clue myself...I reduced this to a single arginine residue, in the
attached pqr file. The command "molsurf test8.pqr 0.0" gives the error
message above.

I'm hoping that Paul Beroza (the author of molsurf) can figure this one out.
But anyone else on this list is welcome to give this a go as well!

> By the way, sander can calculate out the surface area of this structure by
> setting GB=1,PB=1,MS=0 in MM/PBSA input file. Results(SA value) from
> sander and molsurf seem identical, I'm wondering what's difference between
> this two methods. Thanks!

I beleive that sander is using a numerical procedure based on icosahedral
partitioning of the vdW surface. This is fine for the SAS (solvent accessible
surface), but does not give the molecule surface (SES), and is not analytical.

Holger (or someone else) can correct me if I am wrong here....


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Received on Wed Jul 13 2005 - 02:53:01 PDT
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