[gmx-users] ATP/Mg+2 parameters

[George Patargias]

Hello Joao

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
force field.

Best
George


> Hello George,
>
> What do you mean by "best"? It really depends on the force-field that you
> are using/intend to use.
>
> Best,
> Jo?o
>
>
> On Fri, Apr 26, 2013 at 4:00 PM, George Patargias
> <gpat at bioacademy.gr>wrote:
>
>> Hello
>>
>> Doe anybody know what is the "best" (the most suitable) set of
>> parameters
>> 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.
>>
>> Thanks.
>>
>>
>> Dr. George Patargias
>> Postdoctoral Researcher
>> Biomedical Research Foundation
>> Academy of Athens
>> 4, Soranou Ephessiou
>> 115 27
>> Athens
>> Greece
>>
>> Office: +302106597568
>>
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>
>
>
> --
> Jo?o M. Damas
> PhD Student
> Protein Modelling Group
> ITQB-UNL, Oeiras, Portugal
> Tel:+351-214469613
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Dr. George Patargias
Postdoctoral Researcher
Biomedical Research Foundation
Academy of Athens
4, Soranou Ephessiou
115 27
Athens
Greece

Office: +302106597568