Prmtop files are VERY compressible - so you can use gzip - or you can make it available on a file sharing service such as dropbox.
All the best
Ross
> On Oct 23, 2015, at 3:41 PM, Marcelo Andrade Chagas <andrade.mchagas.gmail.com> wrote:
>
> Hi Pengfei.
>
> I sent email with .prmtop file.
>
> But I received this email moderator AMBER list.
>
> "...
> our mail to 'AMBER' with the subject
>
> Re: [AMBER] 12-6-4 LJ-type nonbonded model Fe(III)-M(II)
>
> Is being held until the list moderator can review it for approval.
>
> The reason it is being held:
>
> Message body is too big: 16136278 bytes with a limit of 1024 KB
>
> Either the message will get posted to the list, or you will receive
> notification of the moderator's decision. If you would like to cancel
> this posting, please visit the following URL:
>
> ..."
>
>
> How to send your file to try to add the term C4?
>
> 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 18:58 GMT-02:00 Pengfei Li <ambermailpengfei.gmail.com>:
>
>> 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
>>>>
>>>>
>>>> _______________________________________________
>>>> AMBER mailing list
>>>> AMBER.ambermd.org
>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>
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>>> AMBER mailing list
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>>> http://lists.ambermd.org/mailman/listinfo/amber
>>
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Received on Fri Oct 23 2015 - 16:00:04 PDT
