[gmx-users] ATP/Mg+2 parameters

[Abhishek Acharya]

Hello George,
You need to use Antechamber, a software provided by the amber developers
in a free Amber Tools package. That will produce the right parameters for
the Amber force feild.

Cheers
Abhishek


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
>
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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>