AMBER Archive (2004)

Subject: Re: AMBER: atom type for GBSA

From: David A. Case (case_at_scripps.edu)
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:      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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