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
+++++++++++++++++++++++++++++++++++++++++++++
From chernhoe_at_imcb.nus.edu.sg 19 Feb 2003 09:45:12 +0800
Message-id: <1045619113.2005.0.camel.tommy.ima.org.sg>
Date: 19 Feb 2003 09:45:12 +0800
From: chernhoe <chernhoe_at_imcb.nus.edu.sg>
To: AMBER list <amber.heimdal.compchem.ucsf.edu>
Subject: bugfix.33 not online
In-Reply-to: <NGBBJEEFOCLLBFFOPMABIELMCDAA.yongmei.ncat.edu>
I would like to know how to access bugfix.33 on the website. Thanks
Received on Tue Feb 18 2003 - 16:13:51 PST
