Re: [AMBER] Problems with MM_GBSA

From: Daniel Roe <>
Date: Fri, 31 Jan 2014 09:12:23 -0700


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.

Hope this helps,


On Fri, Jan 31, 2014 at 6:18 AM, Joachim Stump <> wrote:

> Dear all,
> over the last days I performed 39 MM_GBSA alanine scan calculations for
> one system.
> Except for the positions of the respective mutated atoms I kept all
> parameters the same.
> However, I faced problems with only two of those alanine scans.
> The output was:
> Use of uninitialized value in multiplication (*) at
> ~/Amber11/p22-at15p27-x86_64-intel12.1up9-intelmpi4.0.3
> /src/mm_pbsa/ line 1424.
> No data for 0+0 MS SURF 0
> I double- and triplechecked my *.top files but couldn't find the problem.
> I also tried AmberTools 12 but the output was the same.
> When I compared the *_com.all.out/ *_rec.all.out/ *_lig.all.out files
> with those from the 37 other calculations, I realized that in one of
> those 3 files of the aborted calculations the "surface area = ***"-line
> for the first snapshot was missing.
> However, the "surface area = ***"-line seemed to be sporadically missing
> in every *_com.all.out/ *_rec.all.out/ *_lig.all.out file for a few
> snapshots in all other calculations but never in the first one.
> Therefore, the calculations were able to continue with the warning:
> WARNING: Missing SURF for MS in 268 -> Taken from 267
> Since for two alanine scan calculations the values were missing already
> in the first snapshot, no previous value could be taken for calculations.
> In the end, I solved the problem by beginning calculations with the
> second snapshot...
> My question now is: Why is the "surface area"-line sometimes missing?
> Does that mean, that my trajectory is corrupt? Or even the whole
> simulation? The produced alanine scan coordinate-files of the respective
> snapshots seemed to be fine.
> Thought, I should share my experience in case someone else is facing
> similar problems.
> Thanks and have a nice weekend,
> Joachim
> --
> Joachim D. Stump
> University of Erlangen-Nuremberg
> _______________________________________________
> AMBER mailing list

Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-6208 (Fax)
AMBER mailing list
Received on Fri Jan 31 2014 - 08:30:03 PST
Custom Search