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
>
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Received on Fri Mar 25 2011 - 12:00:04 PDT
