Hi Vivek,
You can check the SI of the MCPB.py paper: http://pubs.acs.org/doi/abs/10.1021/acs.jcim.5b00674 <http://pubs.acs.org/doi/abs/10.1021/acs.jcim.5b00674>. There is an example of metal organometallic compound there.
I guess MCPB.py can handle your case but the original PDB file for MCPB.py modeling needs to have each zinc ion and each oxygen separated in different residues (with different residue numbers).
Let me know if you have other questions.
Kind regards,
Pengfei
> On Dec 13, 2016, at 11:50 AM, vivek m <vivek.010484.gmail.com> wrote:
>
> Thanks David.
> I read the manual. Followed the tutorial 20 of metal-proteins MD once also.
> I am doubtful as my cluster is a cage like structure.
> I am attaching a image to make things clear.
> Please advice.
>
>
> On Tue, Dec 13, 2016 at 9:04 PM, David A Case <david.case.rutgers.edu>
> wrote:
>
>> On Tue, Dec 13, 2016, vivek m wrote:
>>>
>>> I want to perform molecular dynamics of (ZnO)12 cluster with a
>> protein.
>>> I have drawn the ZnO cluster and performed gaussian optimization to get
>> the
>>> correct geometry and charges. I have also performed docking of ZnO
>> cluster
>>> with my protein. I have also done the protein preparation as described in
>>> the AMBER tutorials.
>>> I do not know how to move ahead from here. How do i prepare the ZnO-
>>> protein prmtop and inpcrd files.
>>
>> See sections 15.7 and 15.8 in the Amber 2016 Reference Manual.
>>
>> ...dac
>>
>>
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Received on Tue Dec 13 2016 - 12:00:02 PST
