[Dock-fans] GB Parameters for metal ions

Gustavo Seabra gustavo.seabra at gmail.com
Mon Dec 5 11:39:38 PST 2016


Thanks!

—
Gustavo Seabra.



> Em 5 de dez de 2016, à(s) 16:24, Robert C. Rizzo <rizzorc at gmail.com> escreveu:
> 
> 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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