AMBER Archive (2003)

Subject: Re: mm_pbsa

From: Holger Gohlke (gohlke_at_scripps.edu)
Date: Tue Feb 18 2003 - 18:13:51 CST

Yongmei Wang wrote:
>
> Hi, I am new to amber and have several questions regarding mm_pbsa.
>
> (1) Has anyone worked out mm_pbsa.pl that works with UHBD software instead
> of Delphi? I don't have a copy of Delphi, only UHBD.
>
> (2) To calculate the Binding energy between a ligand and receptor, do I
> always have to generate snapshot first (01GenerateSnapshot) and then
> calcualte the binding (06Binding_mmpbsa)?

You don't have to do both subsequently in one mm_pbsa run. Rather, I'd
suggest to generate snapshots in one run, check if they are ok, and then
use these snapshots for calculations of free energies, ...

> (3) When I set DC=1, the meaning of symbols in the output statistics file is
> not clear. Is there any explanation out there about the output data when
> DC=1?

"S", "B", "T" at the beginning of the terms stands for sidechain,
backbone, and total, respectively. INT, VDW, ELE are internal energy
(bond, angle, dihedral), van der Waals energy and Coulomb energy. GAS =
INT + VDW + ELE. GB is the polar part to solvation free energy as
determined by GB. GBSUR is the nonpolar part to solvation free energy.
GBSOL = GB + GBSUR. GBTOT = GAS + GBSOL.

Best regards

Holger

>
> Thanks
> Yongmei
>
> ********************************************
> Yongmei Wang
> Associate Professor
> Dept of Chemistry
> North Carolina A&T State University
> Greensboro, NC 27411
> Tel: 336-334-7601 (ext 2021)
> Fax: 336-334-7124
> Homepage: www.chem.ncat.edu/~yongmei
> email: yongmei_at_ncat.edu
> ********************************************* 

-- 
+++++++++++++++++++++++++++++++++++++++++++++
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
+++++++++++++++++++++++++++++++++++++++++++++