[gmx-users] ATP/Mg+2 parameters

[Jesper Sørensen]

HI George,

For AMBER you can use the parameters by Meagher, Redman, and Carlson they were developed with this force field in mind. They are available on the Bryce group amber parameter database below, although you will have to port them to Gromacs format yourself.
http://www.pharmacy.manchester.ac.uk/bryce/amber#cof

Best,
Jesper


On Apr 29, 2013, at 12:57 AM, Abhishek Acharya <aacharya at iitk.ac.in> wrote:

> 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
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> 
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