AMBER Archive (2009)

Subject: [AMBER] binding energy

From: Simon Becker (simon.becker_at_uni-konstanz.de)
Date: Fri Oct 16 2009 - 04:28:39 CDT

Dear all,

with the risk of someone screaming "rtfm!" at me: is there a program
that allows me to calculate the binding energy directly from a pdb-file?

Let me elaborate: I'm aware of 'the Amber way' - generate model,
minimise, production run, ptraj, mm_pbsa.pl, discuss result. Not gonna
happen this time.
I was presented a number of carefully modelled pdb-files (with coot,
lol), not to be altered, and instructed to calculate the binding energy
between protein and peptide. Ok, me sais, less work for me - or so i
thought. Unfortunately docking tools only envaluate structures they
generated themselves.

So, Ambers, is there a programm/tool/script I load a pdb file to, and
get preferably one number to be copypasted to email, without having to
read a manual that lets the baroque cycle look tiny?

truly yours
Simon 

-- 
Simon Becker
Dept. of Biology
Molecular Bioinformatics
Box M647 
Universitaet Konstanz
D-78457 Konstanz 

mail: simon.becker_at_uni-konstanz.de
Tel: 0049 7531 882900, Fax: 3183

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