The system is not very large--a 450 residue protein with around 13000 water
molecules in the box. The minimization stops at the maximum number, which
is 10000. I'm using a much bigger number now and hopefully the minimization
can finish before hitting this number. Thanks.
On Apr 30, 2011 5:31pm, Bill Miller III <brmilleriii.gmail.com> wrote:
> 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Sat Apr 30 2011 - 16:00:03 PDT
