Re: [AMBER] Interpreting energy decomposition in Amber thermodynamic integration

From: David A Case <>
Date: Fri, 20 Jan 2017 12:25:05 -0500

On Fri, Jan 20, 2017, Stefan Ivanov wrote:
> I would like to ask a few questions relating to the energy
> decomposition in TI with Amber.

Just to be clear: are you running sander/TI with the idecomp flag set?

A couple of other points:

1. Any single TI energy doesn't mean much: you always have to construct
thermodynamic cycles and compare two different legs of the cycle in order
to extract meaningful values; this is the case for both the total energy and
for its decomposition. But it wasn't clear to me exactly which comparisons
you are looking at (i.e. which cycle you are analyzing.)

2. The total free energy change obtained in the TI calculation is indepedent
of the path used through lambda-space (assuming perfect sampling); but the
decomposition is not independent of path. So, interpreting decomposition
results only makes good sense if you know you are using a "same path"
(whatever that means) in various circumstances.

> I am performing TI, transforming one strong protein binder to
> another. All protein internal energies are 0, whereas the internal
> energy for the template ligand and modeled ligand is strongly
> negative. Why are internal energies non-zero only for the ligands?

This results sounds wrong, but I'm not sure exactly what calculation you are
reporting the results of.

> In the .out files, are energy values relative or absolute? I.e., if the
> vdw value for a given residue at λ = 0.9 is negative and positive at
> λ = 0.1, are those values absolute or relative? Are they in kJ/mol or
> kcal/mol?

I'm unsure of your definition of the terms "relative" and "absolute" here.
All Amber energies are in kcal/mol.

Maybe others on the list can give better answers here: my experience with TI
decomposition is pretty limited, for reason 2 above.


AMBER mailing list
Received on Fri Jan 20 2017 - 09:30:02 PST
Custom Search