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
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
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Received on Thu Sep 15 2011 - 09:00:03 PDT
