[Dock-fans] GB Parameters for metal ions

Robert C. Rizzo rizzorc at gmail.com
Mon Dec 5 11:24:12 PST 2016


Dear Gustavo:

Many of the gbradii in the DOCK vdw definition file for common elements
were originally taken from the AMBER7 suite of programs as outlined in
outlined in "Estimation of Absolute Free Energies of Hydration Using
Continuum Methods: Accuracy of Partial Charge Models and Optimization of
Nonpolar Contributions", Rizzo RC, Aynechi T, Case DA, Kuntz ID., J Chem
Theory Comput. 2006 Jan;2(1):128-39. doi: 10.1021/ct050097l.

I haveasked Dwight in our group to look into where values for the other
elements were taken from but my guess is they are from the amber
99 parameter file.  We are checking.


Rob


Robert C. Rizzo, Ph.D., Professor
Department of Applied Mathematics & Statistics,
Institute of Chemical Biology & Drug Discovery,
Laufer Center for Physical & Quantitative Biology
Stony Brook University
Stony Brook NY, 11794-3600
Cell: (631) 944-2891
Office: (631) 632-9340
Fax: (631) 632-8490
rizzorc at gmail.com
http://ringo.ams.sunysb.edu/~rizzo

On Wed, Nov 30, 2016 at 10:05 PM, Gustavo Seabra <gustavo.seabra at gmail.com>
wrote:

> Dear all,
>
> I wonder if anyone can tell me how the gbradii parameters for metal
> cations, present in the vow definition files,  were obtained.
>
> I looked in the manual, and it mentions the parameters as being from
> “Tsui, et al. Biopolymers 2001”. However, I could find no parameters in
> this publication.
>
> Thanks,
>> Gustavo Seabra.
>
>
>
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