On Tue, Mar 26, 2002, dkon_at_email.arizona.edu wrote:
>
> Why can't AMBER (6) handle belly and igb=1?
It is not trivial to combine GB with frozen atoms, and the code has never
been incorporated into Amber. The issues involved are discussed in:
%A O. Guvench
%A J. Weiser
%A P. Shenkin
%A I. Kolossvary
%A W.C. Still
%T Application of the Frozen Atom Approximation to the GB/SA Continuum Model
for Solvation Free Energy
%J J. Computat. Chem.
%V 23
%P 214-221
%D 2002
> What is the proper combination
> of options to run a restrained simulation with continuum solvent, but not
> with "vacuum" options like igb=2 or 3?
Use ntr=1, not ibelly=1.
...regards...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
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Received on Tue Mar 26 2002 - 15:07:33 PST
