AMBER Archive (2003)

Subject: Re: question about MM-PBSA?

From: Holger Gohlke (gohlke_at_scripps.edu)
Date: Thu Apr 17 2003 - 20:31:31 CDT

Hi,

below is a part of an xxx.all.out file for one snapshot:

 BOND = 726.7953 ANGLE = 1139.2334 DIHED =
1424.1961
 VDWAALS = -1492.5262 EEL = -16921.6981 EGB =
-977.9217
 1-4 VDW = 799.5565 1-4 EEL = 10512.9806 RESTRAINT =
0.0000
corrected reaction field energy: 0.0000 kt
 corrected reaction field energy: -3847.462 kt
surface area = 9212.468

* The first three lines are output from the sander calculation.
BOND+ANGLE+DIHED gives the internal energy, the sum of both EEL terms
gives the gas-phase electrostatic energy, and EGB is the polar part of
solvation free energy as calculated by a GB model.
* The "corrected reaction field energy" is the polar part to solvation
free energy in units of kT as calculated with delphi. The first of these
lines is there for the special case that somebody wants to use an
internal dielectric constant other than 1.
* The surface area is given in A^2 and is multiplied afterwards with the
proper beta and gamma values to get the nonpolar part to solvation free
energy according to the continuum model used to determine the
electrostatic part.

I hope this is what you were looking for?

Best regards

Holger

Lishan Yao wrote:
>
> Hi:
> I have a question about the output of MM-PBSA. What are those numbers
> in xxx.all.out files? I couldn't find any description from the manual.
>
> 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
+++++++++++++++++++++++++++++++++++++++++++++