Hi,
(I posted this question last week and didn't get any response. I am
still wondering if anyone else has encountered this problem.)
I ran a one step, energy calculation using the PB option using
mmpbsa_py_energy and sander in Amber 11 on the same conformation of a
protein-ligand complex.
The mdin files were generated by the MMPBSA.py program using default
parameters .
The output matched for all except the EPB term which differed by about
30kcal/mol (-4452 vs -4489).
I ran a similar test with the GB option on the same conformation. In
this case the output matched for all except for the ESURF term, which
differed by about 12kcal./mol
The MMPBSA.py script in Amber11 uses mmpbsa_py_energy if no energy
decomposition is requested. If decomposition is requested, it uses
sander. So, for the same coordinates, if we run MMPBSA free energy
calculations with and without decomposition, you get different results.
Could anyone advise me what I am missing here?
Thanks,
Dam
********************************************************
This communication and any files transmitted with it
may contain information that is confidential, privileged
and exempt from disclosure under applicable law. It is
intended solely for the use of the individual or entity
to which it is addressed. If you are not the intended
recipient, you are hereby notified that any use,
dissemination or copying of this communication is
strictly prohibited. If you have received this
communication in error, please notify the sender.
Thank you for your co-operation.
********************************************************
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed May 09 2012 - 16:30:03 PDT
