Dear all,
I just started today with MMPBSA.py (until now I used mm_pbsa.pl).
After the relevant tutorial and brief reading of MMPBSA.py manual I have
these two questions.
#1
How to proceed with MMPBSA.py if I want to calculate just (absolute) free
energy of the given molecule
(not dG of binding between receptor and ligand molecules).
In case of mm_pbsa.pl one could set just COMPLEX, RECEPTOR, LIGAND flags
in input file like this:
COMPLEX 0
RECEPTOR 1
LIGAND 0
and mm_pbsa.pl will consider here the stand-alone molecule provided as
the "formal receptor" without any complains
that complex or ligand are not specified and calculate just H or S of that
molecule. Is there any way how to
tell MMPBSA.py that I want just calculate H, S or whole G for the given
molecule ?
#2
In mm_pbsa.pl there is available flag PARALLEL which is very useful as it
allows to define howmany frames
from the given trajectory will be processed simultaneously. So for example
if one has node
with 8 CPU cores, setting:
PARALLEL 8
allow to process 8 MD frames simultaneously (probably without need of MPI
?).
In case of python version just usage of MMPBSA.py.MPI instead MMPBSA.py
brings the similar
possibility am I right ?
Thanks in advance for any relevant comment !
Best wishes,
Marek
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Received on Thu Sep 29 2011 - 15:00:02 PDT
