Can't you just use the indicated ZAFF residues to bond to, and bond the
second ion like the first?
bond mol.98.ZN mol.34.SG #Bond zinc ion with SG atom of residue CYM34
bond mol.98.ZN mol.37.SG #Bond zinc ion with SG atom of residue CYM37
bond mol.98.ZN mol.50.NE2 #Bond zinc ion with SG atom of residue HID50
bond mol.98.ZN mol.54.SG #Bond zinc ion with SG atom of residue CYM54
Bill
On 10/7/17 1:58 PM, Parthiban Marimuthu wrote:
> Hi,
>
> I think you have mistaken.
> For the protein that i am working with, it is more appropriate to follow
> ZAFF tutorial.
> http://ambermd.org/tutorials/advanced/tutorial20/ZAFF.htm
>
> Except the fact that, its got two metal centre, like i explained in my
> previous email, 2 times (Zn-CCCC) of Metal centre type 1. For Eg. pls find
> attached the protein model.
>
> The tutorial works fine for one Zn-CCCC metal centre. I am seeking to apply
> the same for more than one of same metal centre type.
>
> Any suggestions..?
>
> Best, Parthiban.
>
>
>> Message: 7
>> Date: Sat, 07 Oct 2017 02:59:06 +0000
>> From: Amani Eshtiwi <eshtiwia2017.gmail.com>
>> Subject: Re: [AMBER] System preparation for protein with Multiple
>> Zn-CCCC
>> To: AMBER Mailing List <amber.ambermd.org>
>> Message-ID:
>> <CAGx4e6DCAxBQ3S6Vz4StX7WNE0CQ53WOR5nJJ0xH_fnrOix-ig.mail.
>> gmail.com>
>> Content-Type: text/plain; charset="UTF-8"
>> Hi Parthiban
>>
>> You can use the MCPB.py tool of AmberTools 16 or 17. I used it for my
>> protein which also has two zinc ions though with coordinating residues
>> other than cysteine. It is easy to use and you can follow the Amber
>> tutorial available here
>> http://ambermd.org/tutorials/advanced/tutorial20/mcpbpy.htm
>>
>> Regards
>> Amani
>>
>>
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Received on Sat Oct 07 2017 - 17:00:02 PDT
