AMBER Archive (2003)

Subject: Questions about statistics output of mm_pbsa?

From: Lishan Yao (yaolisha_at_msu.edu)
Date: Thu May 22 2003 - 16:04:04 CDT

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?
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?
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?

Sincerely
Lishan