AMBER Archive (2003)

Subject: Re: Questions about statistics output of mm_pbsa?

From: Holger Gohlke (gohlke_at_scripps.edu)
Date: Thu May 22 2003 - 16:41:32 CDT

Lishan Yao wrote:
>
> Hi there:
> I did an energy decomposition for one system composed of one
> organic molecule and several thousand water moleules. I got a statistics
> output, but I have some questions about that.
> 1, What is the unit of all those numbers?

The energy values are given in kcal/mol.

> 2, There are four parts in the output: complex, receptor, ligand, and
> delta. It seems to me that in complex part for each residue, I get the
> internal energy and the interaction energy between this residue and all
> the residues around it, in receptor part for each receptor residue, I
> get the internal energy and interaction energy between this residue and
> all the receptors around it, and in ligand part, for each ligand
> residue, I get the internal energy and interaction energy between this
> residue and all other ligand residues around it. In the delta part, it
> gives me the energy difference between complex part and receptor part,
> or between complex part and ligand part. Then those numbers in delta
> part should be the interaction energy between receptors and ligands. Is
> it right?

This is true only for the (pairwise) ELE and VDW terms (and if the
conformations of receptor and ligand don't change on going from the
unbound to the bound state). In the case of GB (although I don't know if
you apply it here), binding of a ligand to a receptor also has an
influence on the self-energy term.

> 3, If number 2 is right, the inteaction energy among water molecules is
> about -0.2~-0.6, as I get. Then the unit should not be kcal/mol. Again
> what's the unit?

It's still kcal/mol.

Best regards

Holger

>
> Sincerely
> Lishan 

-- 
+++++++++++++++++++++++++++++++++++++++++++++
Dr. Holger Gohlke
Dept. of Molecular Biology, TPC15
The Scripps Research Institute
10550 N. Torrey Pines Rd.
La Jolla CA 92037  USA
phone: +1-858-784-9788
fax:   +1-858-784-8896
email: gohlke_at_scripps.edu
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