The *more* likely explanation (rather than minimized snapshots) is that you
didn't have enough memory for the calculation. Normal mode calculations
require a lot of memory compared to the energy calculations.
Good luck!
Jason
On Tue, Nov 9, 2010 at 9:03 PM, Bill Miller III <brmilleriii.gmail.com>wrote:
> Check the nmode ouput (_MMPBSA_*_nm.out) files for more information. The
> exact nature of the error should be able to be found in one or all of the
> _MMPBSA_complex_nm.out, _MMPBSA_receptor_nm.out, or _MMPBSA_ligand_nm.out
> files.
>
> Without information from these files it is difficult to diagnose the
> problem.
>
> Good luck!
>
> -Bill
>
> On Tue, Nov 9, 2010 at 7:08 PM, Khaled Barakat <kbarakat.ualberta.ca>
> wrote:
>
> > Hi all,
> >
> > I'm using the python version of mmpbsa to estimate the entropic
> > contribution of the binding energy for a protein-dna complex. I
> > followed the tutorial posted in the amber website.
> >
> > Any help is appreciated.
> >
> > Khaled
> >
> > Here is my input file:
> >
> >
> > Input file for running entropy calculations using NMode
> > &general
> > endframe=1000, keep_files=2,
> > /
> > &nmode
> > nmstartframe=1, nmendframe=1000,
> > nminterval=500,
> > /
> >
> >
> > and here is my output:
> >
> > | nmstartframe=1, nmendframe=1000,
> > | nminterval=500,
> > |/|--------------------------------------------------------------
> > |Solvated complex topology file: ../../start.prmtop
> > |Complex topology file: ../../complex.prmtop
> > |Receptor topology file: ../../protein.prmtop
> > |Ligand topology file: ../../DNA.prmtop
> > |Initial mdcrd(s): ../run.mdcrd
> > |
> > |Best guess for receptor mask: ":1-195"
> > |Best guess for ligand mask: ":196-237"
> >
> > |Calculations performed using 1000 frames.
> > |NMODE calculations performed using 2 frames.
> > |
> > |All units are reported in kcal/mole.
> > |All entropy results have units kcal/mole (Temperature has been
> > multiplied in as 300 K).
> >
> >
> -------------------------------------------------------------------------------
> >
> >
> -------------------------------------------------------------------------------
> > 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.
> >
> > _______________________________________________
> > 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
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Wed Nov 10 2010 - 07:30:03 PST
