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
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Received on Tue Nov 09 2010 - 18:30:02 PST
