AMBER Archive (2003)

Subject: Re: question about MM-PBSA?

From: Lishan Yao (yaolisha_at_pilot.msu.edu)
Date: Fri Apr 18 2003 - 09:10:24 CDT

Hi:
   I am sorry I didn't make it clear. I want to know what are those
numbers in xxx_lig.all.out,for example:
MM
GB
MS
1
TDC 1 -442.789 -2.940 168.946 -37.666 278.644
SDC 1 -442.789 -2.940 168.946 -37.666 278.644
BDC 1 0.000 0.000 0.000 0.000 0.000
What are they?
Thanks.

Lishan

On Thu, 2003-04-17 at 21:31, Holger Gohlke wrote:
> 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
> +++++++++++++++++++++++++++++++++++++++++++++
>