Thanks for the tip I'l try that.
BR,
Toomas
On 18 Nov 2013 18:41, "Carlos Simmerling" <carlos.simmerling.gmail.com>
wrote:
> 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 <toomaskaevand.gmail.com
> >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 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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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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Received on Mon Nov 18 2013 - 09:00:03 PST
