Re: [AMBER] Problems with MM_GBSA

From: Jason Swails <>
Date: Fri, 31 Jan 2014 12:09:55 -0500

On Fri, 2014-01-31 at 09:12 -0700, Daniel Roe wrote:
> Hi,
> I think that the surface area term used in MMGBSA is LCPO - that being the
> case you can check your trajectory with cpptraj:
> parm <topology>
> trajin <trajectory> 1 5 # Reads in first few frames only
> surf <mask> out surf.dat
> Where <topology> is your topology file, <trajectory> is your trajectory
> file, and <mask> is an atom mask selecting your atoms of interest (your
> receptor and/or ligand). You can see if cpptraj gives you strange results
> as well or something that makes sense. If there are strange results you may
> have corruption in your trajectory. Cpptraj does some checking for
> corruption as well so it may print messages to that effect if the
> trajectory has issues. (FYI - you can also try the 'molsurf' command to get
> the Connolly surface area, although this is not used in MMGBSA I think).
> You can also try and check the surface area by post-processing the
> trajectory with SANDER using imin=5, gbsa=1, and surften=1.0.

Actually for decomposition it uses the gbsa=2 (ICOSA) method to compute
surface areas (it gives better decomposed surface areas, I believe).
LCPO can actually give negative numbers if you try to decompose it :).

AFAIK you need to use gbsa=2, surften=1.0, imin=5 in sander to compute
individual values (i.e., cpptraj has not yet implemented the ICOSA SA

All the best,

Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Fri Jan 31 2014 - 09:30:03 PST
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