Re: [AMBER] Total interaction energy between monomeric units of a dimer

From: anu chandra <>
Date: Thu, 20 Aug 2015 12:04:10 +0100

 Do we have any utility in latest versions of Amber, which do calculations
what 'anal' did in older versions of Amber?. In other words, is it possible
to do group decomposition of energy in, i.e total interaction
energy between two groups, say group A (residue 1-100) and group B (residue
200-250) or group A (residue 50 ) and group B (residue 200-250)?. I noticed
that 'anal' does this sort of decomposition of total energy and I wonder
why Amber has completely removed 'anal' from its 10th version onwards.

Many thanks

On Wed, Aug 19, 2015 at 5:22 PM, David A Case <>

> On Wed, Aug 19, 2015, George Tzotzos wrote:
> >
> > Assuming a GB calculation, would it be legitimate to treat one of the
> > subunits (say subunit A) as a receptor and the other as ligand.
> Yes: the terms "ligand" and "receptor" are just labels. Any problem that
> has
> A + B interacting non-covelently can in principle to addressed by these
> methods.
> > Generate
> > topologies for ligand, receptor and complex using and
> > then run to calculate deltaG of subunit B.
> This gets you the free energy of interaction, not the free energy of
> interaction "of subunit B". It doesn't matter which subunit you call
> "ligand"
> and which one you call "receptor".
> > Repeat same procedure (using subunit B as receptor) to calculate deltaG
> of
> > subunit A. Would adding the deltaGs of the two subunits correspond to
> > the total interaction energy?
> There is no need to repeat anything. The two calculations you describe are
> identical. [If not, them I am not understanding what you are proposing to
> do.]
> ....dac
> _______________________________________________
> AMBER mailing list
AMBER mailing list
Received on Thu Aug 20 2015 - 04:30:03 PDT
Custom Search