Based on the names of these files, it looks like you have an outdated
version of MMPBSA.py. We no longer use sander to minimize for entropy
calculations, but instead use a nab program that uses a better minimizer.
You can download the updated version of MMPBSA.py with installation
instructions from the tutorial website (
http://ambermd.org/tutorials/advanced/tutorial3/py_script/). Also, do not
forget to apply the patches.
This should hopefully help fix your problem.
-Bill
On Fri, Mar 25, 2011 at 2:39 PM, amit dong <dongamit123.gmail.com> wrote:
> The _MMPBSA_nmode_mincom.mdouts, _MMPBSA_nmode_minrec.mdouts and
> _MMPBSA_nmode_minlig.mdouts ended way before 50K steps. They reached RMSD
> ~9.6828E-05 in that time.
>
> On Fri, Mar 25, 2011 at 1:23 PM, Bill Miller III <brmilleriii.gmail.com
> >wrote:
>
> > It looks like your system is not minimizing quick enough to reach the
> > requested drms. Did the _MMPBSA*_nm.out all reach 50,000 minimization
> steps
> > before ending? If so, you might want to try increasing maxcyc accordingly
> > to
> > allow more cycles for the minimizer to reach the desired rms.
> >
> > -Bill
> >
> > On Fri, Mar 25, 2011 at 2:12 PM, amit dong <dongamit123.gmail.com>
> wrote:
> >
> > > Hi,
> > >
> > > I am running nmode calculations (Amber11, python script, serial
> version)
> > on
> > > a complex with ~500atoms. I get the following results:
> > >
> > >
> > > ENTROPY RESULTS (HARMONIC APPROXIMATION) CALCULATED WITH NMODE:
> > >
> > > Complex:
> > > 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
> > >
> > >
> > > Receptor:
> > > 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
> > >
> > >
> > > Ligand:
> > > 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
> > >
> > >
> > > The MMPBSA_complex_nm.out, _MMPBSA_receptor_nm.out, or
> > > _MMPBSA_ligand_nm.out
> > > files end abruptly without error. They end with
> > >
> > > Root-mean-square gradient of input coords is 0.244797413344676
> > > This is greater than the requested maximum: 1.000000000000000E-003
> > >
> > >
> > > My input file is:
> > >
> > > &general
> > > endframe=50000000000, verbose=1, initial_traj=1,
> > > /
> > > &nmode
> > > nmstartframe=1, nmendframe=7200,
> > > nminterval=720,
> > > maxcyc=50000, drms=0.0001,
> > > /
> > >
> > >
> > > I would be really grateful if anyone could help me troubleshoot the
> > issue.
> > > I
> > > am sure memory is not an issue since I am using 12GB for my system with
> > > about 500 atoms. The snapshots I am using are from post 5ns MD.
> > >
> > > Thanks
> > > Amit
> > > _______________________________________________
> > > 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 Fri Mar 25 2011 - 12:30:03 PDT
