Re: AMBER: GB parameters for Calcium

From: David A. Case <case.scripps.edu>
Date: Wed, 23 Jun 2004 11:10:23 -0700

On Wed, Jun 23, 2004, cailliez wrote:
>
> Anyway for all the cases I made, results are quite similar with
> correlation coefficient of 0.98 between GB and PB.
> For all cases, we thus can write E(PB)=A*E(GB)+B, with A=0.96-0.97.
>
> The big difference is for B. which vary from 300 to 660 kcal/mol,
> depending which Born radius I take.

This is in accord with what we find as well. See esp. Fig. 3 in:

%A H. Gohlke
%A D.A. Case
%T Converging Free Energy Estimates: MM-PB(GB)SA Studies on the
Protein-Protein Complex Ras-Raf
%J J. Comput. Chem.
%V 25
%P 238-250
%D 2004

> How can I know which choice is the best (if there is one...) ?

....good luck! :-) ...dac 

-- 
==================================================================
David A. Case                     |  e-mail:      case.scripps.edu
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
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10550 N. Torrey Pines Rd.         |  home page:                   
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Received on Wed Jun 23 2004 - 19:53:01 PDT
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