A couple more comments:
On Sun, Sep 22, 2013 at 7:13 PM, sudipta <sudipta.mml.gmail.com> wrote:
> [snip]
>
>
> Do I need to use ante-MMPBSA.py program for generating the .prmtop file
> for running MMPBSA.py.MPI program. If so how do I use that? Is there any
> significant difference between AMBERtools12 and AMBERtools13 for running
> MMPBSA.py.MPI program
No, ante-MMPBSA.py is never necessary if you create all of the needed
topology files in the beginning, prior to running any calculations (as is
recommended practice). ante-MMPBSA.py is particularly useful when you
decide to do MM/PBSA calculations on a system after creating the topology
file and you don't happen to have the files you need to create them through
tleap.
However, ante-MMPBSA.py does _not_ work with chamber-generated topology
files, so that's not even an option in your case. As for the 12 vs. 13
difference, AmberTools 13 has more bug fixes and more stable PBSA options
than AmberTools 12 in terms of the default solvation radii for the
non-polar solvation free energy part of the calculation.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Mon Sep 23 2013 - 04:30:02 PDT
