How large is your system? Also, did the minimization stop when it hit the
maximum number of minimization steps, or did it end before that? What is the
maximum number of minimization steps you are specifying in your input file?
You could always try increasing this in your input file if the minimization
stops only after hitting this maximum so that you perform more minimization.
-Bill
On Sat, Apr 30, 2011 at 6:17 PM, <anyiphysics.gmail.com> wrote:
> 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
>
> > http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> 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 Sat Apr 30 2011 - 16:00:02 PDT
