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
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Received on Tue Nov 06 2012 - 22:30:03 PST
