Hi Marcelo,
Actually you can add C4 to two types of metal by using add12_6_4 command in ParmEd. In that case you need to use one ambermask to represent the two ions in the command line. But there may be some bugs in the former code and I am not sure the updates of AmberTools15 have fixed it or not. You can also send me the topology file for adding C4 term and I can help to add the C4 terms for you.
Are you going to investigate the ligand exchange in the coordination shell? If not, you can also try to build the bonded model using MCPB.py, here is the related tutorial: http://ambermd.org/tutorials/advanced/tutorial20/mcpbpy.htm <http://ambermd.org/tutorials/advanced/tutorial20/mcpbpy.htm>.
Best,
Pengfei
> On Oct 22, 2015, at 3:24 PM, Marcelo Andrade Chagas <andrade.mchagas.gmail.com> wrote:
>
> Hi Pengfei,
>
> I was thinking here, and I began to doubt what made so far in this case.
>
> I guess my first question should have acid: you can enter the term C4
> the ion model is not connected 04/06/12-LJ for a system that has the active
> site
> a metallic center type (Fe (III) -M (II)?
>
> Was studying the model again in A20 tutorial and it seems to me only
> One can add the term C4 to active sites with only one type of metal.
>
> It concludes that correct?
>
> Best regards,
>
> Marcelo
>
> 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
>
> 2015-10-22 12:36 GMT-02:00 Pengfei Li <ambermailpengfei.gmail.com>:
>
>> Hi Marcelo,
>>
>> What residues coordinate to the Fe(III) and Zn(II) ions?
>>
>> Best,
>> Pengfei
>>
>>> On Oct 22, 2015, at 10:34 AM, Marcelo Andrade Chagas <
>> andrade.mchagas.gmail.com> wrote:
>>>
>>> Dear AMBER of the list,
>>>
>>> How to use unbound ion model described in the tutorial:
>>>
>>> 12-6-4 LJ-type nonbonded model in the AMBER,
>>>
>>> to systems like proteins Fe(III)-M(II) ...M=Zn(II)?
>>>
>>> Best regards,
>>>
>>> Marcelo
>>>
>>> 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
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
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Received on Thu Oct 22 2015 - 14:00:03 PDT
