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://amber.ch.ic.ac.uk
> 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.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
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Received on Mon Jun 02 2003 - 01:53:01 PDT
