AMBER Archive (2004)

Subject: Re: AMBER: atom type for GBSA

From: David A. Case (
Date: Wed Feb 11 2004 - 11:33:04 CST

On Wed, Feb 11, 2004, aini_at_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: 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 | ================================================================== ----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to To unsubscribe, send "unsubscribe amber" to