AMBER Archive (2003)

Subject: mm_pbsa

From: Yongmei Wang (yongmei_at_ncat.edu)
Date: Tue Feb 18 2003 - 17:14:01 CST

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)?

(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?

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
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