What version of MMPBSA.py are you using? The newest version was just
released with AmberTools 1.5. So if you are not using this version, I would
strongly urge you to download AmberTools 1.5 and use that version because it
has many new features and bugfixes from previous versions.
This message can sometimes be a memory issue, but it can also be something
else. Do you have reason to believe this could be a memory issue? For an
average system, I have found that an nmode calculation can take ~2.5 GB of
memory. If you are running this in parallel, then you will obviously need
more considering you will be running multiple calculations at once. Also, if
you have a relatively large system, the calculation could also take quite a
bit more memory. But if this is an issue, you should find some error message
about a lack of memory in one of the output files (most likely the standard
error and out files). You should also investigate the MMPBSA.py output
files. In particular, the minimization output file and nmode output files
(if any were created). If this is actually a minimization problem, then
there should be such a message in one (or more) of the _MMPBSA_*_nm.out
files.
I hope that helps. It is somewhat difficult to diagnose this problem without
more information.
-Bill
On Fri, Apr 29, 2011 at 4:29 PM, Yi An <anyiphysics.gmail.com> wrote:
> Hi AMBER users,
>
> I managed to use MMPBSA to calculate the binding free energy between a
> small
> DNA molecule and an anti-DNA antibody. I also tried to calculate the
> entropy
> with normal mode analysis. However, none of these calculations finished
> normally. In a lot of cases, I got such none-sense numbers:
>
> "Entropy Term Average Std. Dev.
> ------------------------------
> -----------------------------
> Translational: -1.0000 0.0000
> Rotational: -1.0000 0.0000
> Vibrational: -1.0000 0.0000
> Total: -1.0000 0.0000
>
>
> DELTA S total= 1.0000 +/- 0.0000
>
> -------------------------------------------------------------------------------
>
> -------------------------------------------------------------------------------
>
> WARNINGS:
> Not all of your snapshots minimized within tolerable limits for nmode"
>
>
> And in the log.error file , "Warning: Not all of your snapshots minimized
> within tolerable limits for nmode" showed up again.
>
> Is it a memory issue? If not, how could I fix this problem?
>
> Yi An
>
> Graduate student
> Department of Chemistry
> Texas A&M University
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Bill Miller III
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-6715
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Received on Fri Apr 29 2011 - 20:00:03 PDT
