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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Received on Thu Sep 15 2011 - 05:30:02 PDT
