On Thu, Sep 15, 2011 at 11:34 AM, Antje Wolf
<antje.wolf.scai.fraunhofer.de>wrote:
> The differences in the FINAL_RESULTS_MMPBSA.dat are:
>
> Energy Component Average Std. Dev. Std. Err. of
> Mean
>
> -------------------------------------------------------------------------------
> 1-4 VDW -2.2416 0.5667
> 0.0567
> 1-4 EEL -1.4070 0.0306
> 0.0031
>
Yea, I would say that is an unacceptable difference. I've never seen this
behavior before... If this is a bug, though, it's a bug in sander since all
MMPBSA.py does is parse the sander output
>
> But the final deltaG differs by 6 kcal/mol depending on if I include
> &decomp or not. That is quite a lot.
>
> Antje
>
> ----- Ursprüngliche Mail -----
> | 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
> | >
> | > _______________________________________________
> | > AMBER mailing list
> | > AMBER.ambermd.org
> | > http://lists.ambermd.org/mailman/listinfo/amber
> | >
> |
> |
> |
> | --
> | Jason M. Swails
> | Quantum Theory Project,
> | University of Florida
> | Ph.D. Candidate
> | 352-392-4032
> | _______________________________________________
> | AMBER mailing list
> | AMBER.ambermd.org
> | http://lists.ambermd.org/mailman/listinfo/amber
> |
>
> --
> 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
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> 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 - 10:30:03 PDT
