[AMBER] Problems with MM_GBSA

From: Joachim Stump <joachim.stump.biochem.uni-erlangen.de>
Date: Fri, 31 Jan 2014 14:18:31 +0100

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
/src/mm_pbsa/mm_pbsa_statistics.pm 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 D. Stump
University of Erlangen-Nuremberg
AMBER mailing list
Received on Fri Jan 31 2014 - 05:30:04 PST
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