If you're actually keeping the water, I'm writing this minimization off as
hopeless. Moreover, I can't imagine any normal mode calculation will have
enough memory to run such a massive system (even 450 residues with no water
will require a lot of memory, but add in 13000 water molecules and all bets
are off).
Moreover, I don't know how much sense it makes to include water in a normal
mode calculation...
All the best,
Jason
On Sun, May 1, 2011 at 12:36 AM, <anyiphysics.gmail.com> wrote:
> 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
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
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Received on Sun May 01 2011 - 04:00:04 PDT
