Hi Jason,
I have sent all the related files for running the MMPBSA.py.MPI program to
you. Please take a look on those whenever you are free. Also let me know if
you need any further information from my side.
Best
sudipta
On Mon, Sep 23, 2013 at 7:04 AM, Jason Swails <jason.swails.gmail.com>wrote:
> 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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>
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Received on Mon Sep 23 2013 - 10:30:02 PDT
