Actually, MMPBSA.py will use imin=5. If you want the GB and/or PB
energies, then by all means use MMPBSA.py. However, if you want to use
boundary conditions, you'll need to use sander with imin=5.
One nice thing about MMPBSA.py if it calculates what you want is that it
will output the data (optionally) into a CSV-formatted file.
Good luck,
Jason
On Wed, Nov 7, 2012 at 1:24 AM, Aron Broom <broomsday.gmail.com> wrote:
> oh wow, thanks. I really did look over the manual before asking that, but
> as it's quite clearly stated, I have no excuses. Thanks for the reply :)
>
> On Wed, Nov 7, 2012 at 1:09 AM, Roitberg,Adrian E <roitberg.ufl.edu>
> wrote:
>
> > look in the manual for the imin=5 option in main
> >
> > that should compute the energy and components for every snapshot
> > ________________________________________
> > From: Aron Broom [broomsday.gmail.com]
> > Sent: Wednesday, November 07, 2012 1:07 AM
> > To: AMBER Mailing List
> > Subject: [AMBER] Energy Analysis from Trajectory
> >
> > Hello AMBER users,
> >
> > If I have a trajectory and related parameter/topology files, and want to
> > grab the potential energy for each snapshot in that trajectory (perhaps
> > broken into various components, i.e. EEL and such), is the best option to
> > use MM/PBSA.py? That is, even if I have no plan to break things down
> into
> > receptor and ligand (I just have a single molecule) is it the simplest
> way
> > to go about doing what I'm after, or will it be upset about not being
> able
> > to identify a separate receptor and ligand?
> >
> > Thanks,
> >
> > ~Aron
> >
> >
> >
> > --
> > Aron Broom M.Sc
> > PhD Student
> > Department of Chemistry
> > University of Waterloo
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Aron Broom M.Sc
> PhD Student
> Department of Chemistry
> University of Waterloo
> _______________________________________________
> 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
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Received on Wed Nov 07 2012 - 11:30:03 PST
