Re: [AMBER] can MCPB build non amino-acid containing complex?

From: zoran matovic <>
Date: Fri, 1 Jul 2016 17:13:32 +0200

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 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.


-----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!

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 - 08:30:03 PDT
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