On Wed, Feb 11, 2004, aini.UMDNJ.EDU wrote:
>
> I want to run GBSA simulation on a series of compounds. I knew AMBER
> misses surface parameter for certain atom types, such as halogen atom. Can
> someone tell me where I could find a complete list of atoms that have
> surface parameters in the AMBER.
>
Look for the section "assign parameters for calculating SASA according to
the LCPO method" in amber7/src/mdread.f (about line 664).
> And how could I generate missing parameters?
Depending on the accuracy you need: you could adapt the parameters from
some existing atom type to the one you want; or you could adjust new
parameters to fit surface areas calculated exactly, in the way that the
original parameters were developed (see the LCPO paper for details).
....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 Wed Feb 11 2004 - 17:53:01 PST
