[AMBER] Substructure potential energy

From: Toomas Kaevand <toomaskaevand.gmail.com>
Date: Mon, 18 Nov 2013 18:32:47 +0200

Dear AMBER gurus,

is there any convenient way how to extract potential energy of a protein
substructure (e.g. an enzyme active centre) from pmemd or sander trajectory
files. The problem is that in addition to the whole system energy
information (which we get as an output of pmemd/sander), we also need to
analyse energy changes of a subsystem (e.g. some functional groups which
are belonging to the active centre of an enzyme). In theory it seems to be
possible because we have MD trajectory and parameter files which contain
all necessary data but in practice I haven’t find any usable solution for
the problem.

Currently we are using Amber 12 and AmberTools 13.

Best regards,

Toomas Kaevand

Tallinn University of Technology
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Received on Mon Nov 18 2013 - 09:00:02 PST
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