Dear Rebeca,
If you want to use a nonbonded model, you can use the parameter file just as Marcelo said (the file name may change due to different version of AmberTools, you can check the "Ions” section” in "Molecular mechanics force fields” chapter of the AMBER manual you are using for details).
If you want to use a bonded model, MCPB.py could offer help. I suggest you to download the AmberTools16 (which is free: http://ambermd.org/AmberTools16-get.html <http://ambermd.org/AmberTools16-get.html>) which has a newest version of MCPB.py in it.
BTW, an metal ion modeling tutorial about AMBER could be found here: http://ambermd.org/tutorials/advanced/tutorial20/ <http://ambermd.org/tutorials/advanced/tutorial20/>.
Kind regards,
Pengfei
> On May 13, 2016, at 11:40 AM, Marcelo Andrade Chagas <andrade.mchagas.gmail.com> wrote:
>
> Dear,
>
> if you have installed amber program, you find some parameters
> treat the metal ion using ion model is not connected in the following
> directory
> the amber program:
>
> cd amber14/dat/leap/parm
>
> For example:
>
> vi frcmod.ionslrcm_cm_tip3p
>
> Regards,
>
> Marcelo A. Chagas
>
> Marcelo Andrade Chagas, MSc
> (PhD student)
> Laboratório de Química Computacional e Modelagem Molecular - LQC-MM
> * http://lqcmm.qui.ufmg.br/
> Departamento de Química da Universidade Federal de Minas Gerais - UFMG
> Tel:(31)3409-5776
>
> 2016-05-13 12:14 GMT-03:00 Rebeca García Fandiño <regafan.hotmail.com>:
>
>> Dear Amber users,
>> I am trying to find some parameters for Ni2+ cation to be used in
>> combination with the Amber force-field.
>> Does anybody know where I could find them?
>> Thanks a lot for your help.
>> Best wishes,
>> Rebeca
>>
>> Dr. Rebeca Garcia Fandino
>> Santiago de Compostela University
>> Spain
>>
>>
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>>
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Received on Fri May 13 2016 - 14:00:05 PDT
