[gmx-users] ATP/Mg+2 parameters
gpat at bioacademy.gr
Mon Apr 29 08:50:46 CEST 2013
Thanks for the reply; I am planning to use Amber 99SB-ILDN force field.
I just wanted to know which parameter set is the most suitable for ATP/Mg
(in terms of reproducing the right geometry etc) in conjunction with any
> Hello George,
> What do you mean by "best"? It really depends on the force-field that you
> are using/intend to use.
> On Fri, Apr 26, 2013 at 4:00 PM, George Patargias
> <gpat at bioacademy.gr>wrote:
>> Doe anybody know what is the "best" (the most suitable) set of
>> to use for ATP/Mg+2 ?
>> I have seen from the literature that people have used mainly either the
>> CHARMM27 parameters or the ones in
>> Meagher KL, Redman LT, Carlson HA (2003) Development of polyphosphate
>> parameters for use with the AMBER force field. J Comput Chem 24:1016
>> I would appreciate if you can give me any hints on this.
>> Dr. George Patargias
>> Postdoctoral Researcher
>> Biomedical Research Foundation
>> Academy of Athens
>> 4, Soranou Ephessiou
>> 115 27
>> Office: +302106597568
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> Jo?o M. Damas
> PhD Student
> Protein Modelling Group
> ITQB-UNL, Oeiras, Portugal
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Dr. George Patargias
Biomedical Research Foundation
Academy of Athens
4, Soranou Ephessiou
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