Hey Bill,
Now I'm sure there is a minimization problem because I found the following
at the end of each MMPBSA_*_nm.out file:
"Root-mean-square gradient of input coords is 0.264481725292420
This is greater than the requested maximum: 1.000000000000000E-002"
I just think it's a little dangerous to change the maximum in DRMS... Maybe
I can run a much longer minimization to fix this problem? Thanks a lot.
Yi
On Apr 29, 2011 9:54pm, Bill Miller III <brmilleriii.gmail.com> wrote:
> 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
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Received on Sat Apr 30 2011 - 15:30:02 PDT
