[AMBER] Calculating Energy of an atom selection

From: Aron Broom <broomsday.gmail.com>
Date: Fri, 17 Aug 2012 17:19:28 -0400


I'm interested in pulling out the energy contributions for a selection of
atoms (such as a residue) from a trajectory of a large simulation. That is
to say, I'd like something similar to what you get in the "mden" output
file, but not for the whole system, just a residue I'm interested in. It
seems like that kind of functionality might be provided by the MM-PBSA
utility in ambertools. Does that sound right, is that what others would
do? In the AmberTools manual it is referred to as "stability analysis",
where one only specifies a complex topology and no receptor. Is there a
better way to do this with cpptraj? I'm looking at a system that was
simulated with GBIS, so MM-PBSA seems like it might be an appropriate
choice anyway.

Any suggestions, or should I just try to use MM-PBSA?



Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo
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Received on Fri Aug 17 2012 - 14:30:03 PDT
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