On Fri, Jul 04, 2003, Marco Aurelio Correia Preto wrote:
>
> We are doing some molecular dynamic runs of small non-standart peptides (in
> water) and we would like to do the smae dynamics in other solvents! There
> are a couple of potential for organic solvents, but some of them are rigid
> one! How can we do this in Amber (version 6 is the one we have)? Can we use
> very large force constants to force a rigid conformation?
>
It is more typical to use SHAKE to keep solvent molecules rigid. Some other
solvents (chloroform, methanol, acetonitrile, ...) are available at:
http://pharmacy.man.ac.uk/amber/
...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 Fri Jul 04 2003 - 18:53:00 PDT
