Hi Zhengyu,
You can use MCPB.py to do parameterizations for both the metalloprotein and organometallic compound systems.
There are two examples shown in supporting information 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>. One is metalloprotein and the other is organometallic compound.
Kind regards,
Pengfei
> On Jul 1, 2016, at 11:13 AM, zoran matovic <zmatovic.kg.ac.rs> wrote:
>
> Hi,
> I've never used MCPB to determine ff parameters for metal containing site
> but I believe that is possible. What I suggested u is use of MCPB.py which
> is more straightforward and an independent metal containing unit is possible
> to parameterize for sure. So-called "sidechain" unit (see tutorial) which
> include metal is determined by the M-L distance where M and L have
> predetermined coordinates within system. Therefore u can parameterize any
> complex molecule (charged or not) within Protein-Complex system with metal
> being either connected to amino acid or not.
> It's up to u choose the method.
>
> Cheers
> Zoran
>
>
> -----Original Message-----
> From: Zhenyu Meng
> Sent: Friday, July 1, 2016 2:37 PM
> To: AMBER Mailing List
> Subject: [AMBER] can MCPB build non amino-acid containing complex?
>
> Dear Amber users,
> Recently I'm trying to use MCPB to build a FF for Pt-complex and this
> complex is NOT connected to amino acid.
> The Pt is connected to one amine, one chloride, and 2 N in an aromatic ring.
> I want to know whether MCPB can proceed such complex?
> Your kind help will be highly appreciated!
>
>
> --
> Sincerely,
> Mr. Meng Zhenyu
> Division of Chemistry and Biological Chemistry
> School of Physical and Mathematical Sciences
> Nanyang Technological University
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Received on Fri Jul 01 2016 - 09:00:03 PDT
