AMBER Archive (2003)

Subject: Re: information

From: David A. Case (case_at_scripps.edu)
Date: Sun Jun 01 2003 - 19:14:29 CDT

On Thu, May 29, 2003, aram joel panay wrote:

> I?m interested in calculations of binding energy for protein-protein,
> protein-peptide; a colleague told me the AMBER program might be useful...

> how can I get the software package?

See the amber web page: http://www.amber.ucsf.edu/amber/

> how big are the proteins this program can manage?
> What type of hardware I need to run the program?
> And something very important, how friendly this program is? Because we work
> in molecular biology, but not in physical chemistry, so no one has strong
> skills in the management of this kind of software.

Calculating binding energies for proteins + peptides (and especially for
proteins + proteins) is a very challenging task. It appears that any reliable
calculation of protein/protein association energies is not yet possible, even
for the most experienced users. In any event, you should expect to invest
a significant effort, in learning computers, in learning about simulation
techniques, and in interpreting the data and their probable errors, if you
expect to get any interesting results.

..good luck...dac 

-- 

==================================================================
David A. Case                     |  e-mail:      case_at_scripps.edu
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
10550 N. Torrey Pines Rd.         |  home page:                   
La Jolla CA 92037  USA            |    http://www.scripps.edu/case
==================================================================