Look at your FINAL_RESULTS output file (*not* the decomp). It should print
out the differences in the 1-4 VDW/EEL terms. If they are close to zero,
you should be fine.
How large are those values?
On Thu, Sep 15, 2011 at 8:13 AM, Antje Wolf
<antje.wolf.scai.fraunhofer.de>wrote:
> Dear list,
>
> I am currently doing MM-PBSA calculations using the MMPBSA.py script
> (AmberTools1.5, AMBER11 with all latest bug fixes applied). What bothers me
> is a warning message when I include energy decomposition analysis. For both,
> Generalized Born and Poisson-Boltzmann, the final result file contains:
>
> WARNING: INCONSISTENCIES EXIST WITHIN 1-4 NON-BONDED TERMS.
> CHECK YOUR INPUT FILES AND SYSTEM SETUP. THESE RESULTS MAY NOT BE RELIABLE
> (check differences)!
>
> Here is my mmpbsa.in file:
>
> &general
> endframe=100, verbose=1
> /
> &gb
> igb=2, saltcon=0.100
> /
> &pb
> istrng=0.100,
> /
> &decomp
> idecomp=1, dec_verbose=1,
> print_res="1-217"
> /
>
> When I do NOT include the &decomp namelist, no warning is printed and also
> my final deltaG values are different.
> Can I trust the energy decomposition results? Should I maybe try a
> different idecomp model?
>
> Thanks,
> Antje
>
> --
> Antje Wolf
>
> Fraunhofer-Institute for Algorithms and Scientific Computing (SCAI)
> Department Bioinformatics
> Schloss Birlinghoven
> D-53754 Sankt Augustin
>
> Tel.: +49 2241 14 2552
> E-mail: antje.wolf.scai.fraunhofer.de
> Internet: http://www.scai.fraunhofer.de
>
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Thu Sep 15 2011 - 07:30:05 PDT
