thanks again,
Shashi
On Tue, Feb 26, 2013 at 10:27 AM, Jason Swails <jason.swails.gmail.com>wrote:
> 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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> > >
> >
> >
> >
> > --
> > Shashidhar N. Rao
> > 3 SERINA DRIVE
> > PLAINSBORO
> > NEW JERSEY 08536 USA
> >
> > shashidharr.gmail.com
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> 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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Received on Tue Feb 26 2013 - 08:30:04 PST
