AMBER Archive (2002)

Subject: Re: Gibbs (FEP) (fwd)

From: David A. Case (case_at_scripps.edu)
Date: Mon Aug 26 2002 - 20:30:28 CDT

On Mon, Aug 26, 2002, amber_at_heimdal.compchem.ucsf.edu wrote:
>
> I'm trying to compute the activation free energy (using FEP in Gibbs module)
> of a proton transfer reaction of an enzyme.
>
> I have tried to load the reactant of the reaction (state 0) and the
> Transition State of the reaction (state 0) in leap. I also modified the
> charges and parameters for the state 0. But when I tried to save the parm
> and coord files of the perturbed state 1(saveAmberParmPert), leap complained
> that I was missing some bonds, angles and dihedral parameters concerned with
> dummy atoms.
>
> Can anyone tell me how to create the dummy atoms parameters in order to
> do this?

This is something of an art, and there is no single correct answer (since
these are, after all, dummy atoms.) You might get some ideas from the gibbs
tutorial on the web, or by reading the methods details section of some
published work that is roughly the same as what you want to do. Peter
Kollman's big review would be a good place to start:

%A P. Kollman
%T Free energy calculations: Applications to chemical and biochemical
phenomena
%J Chem. Rev.
%V 93
%P 2395-2417
%D 1993
%K review

..hope this helps....dac 

-- 

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David A. Case                     |  e-mail:      case_at_scripps.edu
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
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