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 - 08:30:03 PDT
