[AMBER] MMPBSA tutorial: MMPBSA.py

From: camm-kansai <ke.gohda.camm-kansai.org>
Date: Tue, 10 Mar 2015 20:32:06 +0900


I am using AMBER14 and AMBERTOOLS14.


I am following the course of MMPBSA tutorial. In the course, I have
encountered a certain discrepancy in the results of MMPBSA calculations
between by MMPBSA.py and by mmpbsa_pl when using the data-set of the ras-raf
system downloaded from the tutorial pages.


My MMPBSA calculation by MMPBSA.py with the default mmpbsa.in for MMPBSA.py
resulted a fairly smaller delta PBTOT vaule than that noted in the tutorial,
i.e., -28.18 kcal/mol vs -86.36 kcal/mol. Contrarily, MMPBSA calculation by
mmpbsa_pl with the default mmpbsa.in for mmpbsa_pl rather reproduced the
tutorial value, -86.28 kcal/mol vs -89.13 kcal/mol, of which difference may
be due to machine-dependency.


To check the installation failure of mmpbsa_py_enery exec-file in my
machine, sander was used for MMPBSA.py by setting the use_sander parameter
to be 1. However, the same discrepant result, -28.11 kcal/mol, was obtained.


Next, the two input files, mmpbsa.in, for MMPBSA.py and mmpbsa_pl in the
tutorial were compared to figure out the cause of the MMPBSA differences.
Then, the followings are found to be different between the two:

- inp (nonpolar optimization method): py =2 whereas pl =1

- istrng (ionic strength in M): py =0.100 whereas pl =0.000


Then, the original mmpbsa.in for MMPBSA.py was modified to align with that
for mmpbsa_pl, i.e., inp=1 and istrng=0.000.


MMPBSA calculation using the modified mmpbsa.in for MMPBSA.py gave quite
identical results to that of mmpbsa_pl, i.e., -87.82 kcal/mol, which seems
to resolve my issue. However, by looking at the AMBER14 manual, it says that
inp=1 is an old method for nonpolar optimization.


I would very much appreciate it if you could give me any suggestions for my
issue on MMPBSA tutorial.


Best wishes,



Keigo Gohda, PhD

Computer-aided Molecular Modeling Research Center (CAMM), Kansai

3-32-302 Tsuto-Otsuka, Nishinomiya, 663-8241 Japan





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Received on Tue Mar 10 2015 - 05:00:03 PDT
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