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
> _______________________________________________
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> 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 - 11:30:05 PDT
