Re: [AMBER] Substructure potential energy

From: Carlos Simmerling <>
Date: Mon, 18 Nov 2013 11:38:54 -0500

yes- look in the manual at the idecomp energy decomposition section. you
could probably use the mm/pbsa scripts as well.

On Mon, Nov 18, 2013 at 11:32 AM, Toomas Kaevand <>wrote:

> 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 havenít 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 - 09:00:03 PST
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