MMPBSA.py will do that for you (using cpptraj).
On Tue, Feb 26, 2013 at 9:56 AM, Shashidhar Rao <shashidharr.gmail.com>wrote:
> thanks, Jason. I guess the trick is to convert my single complex to the
> trajectory.
>
> Shashi
>
> On Mon, Feb 25, 2013 at 8:20 PM, Jason Swails <jason.swails.gmail.com
> >wrote:
>
> > On Mon, Feb 25, 2013 at 4:08 PM, Shashidhar Rao <shashidharr.gmail.com
> > >wrote:
> >
> > > Hello,
> > >
> > > this may be a silly question - but if I wish to run "MMPBSA.py"
> > calculation
> > > on a single complex of a protein with a single ligand (as opposed to a
> > > trajectory), would the suitable flag be "-y" or something else?
> > >
> >
> > The "input trajectory" can be any format recognized by cpptraj -- PDB,
> > mol2, restart, ASCII trajectory with box info, ASCII trajectory without
> box
> > info, NetCDF, dcd, etc.
> >
> > The reason for this flexibility is because MMPBSA.py uses cpptraj
> directly
> > for snapshot preparation ;).
> >
> > HTH,
> > Jason
> >
> > --
> > Jason M. Swails
> > Quantum Theory Project,
> > University of Florida
> > Ph.D. Candidate
> > 352-392-4032
> > _______________________________________________
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> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Shashidhar N. Rao
> 3 SERINA DRIVE
> PLAINSBORO
> NEW JERSEY 08536 USA
>
> shashidharr.gmail.com
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Tue Feb 26 2013 - 08:00:02 PST
