Hi Pengfei,
Thanks for your information.
I follow the instruction in SI of your paper to build my own FF.
Everything goes fine, while a small problem arises:
My structure has a chloride connected to Pt, while using MCPB.py, the
output seems cannot find chloride within the bonding radius:
***Selected Metal ion PT is atom 1 in residue 1-PT
2-RES.N1 is in 2.8 Angstrom of 2-RES.N1
2-RES.N2 is in 2.8 Angstrom of 2-RES.N2
2-RES.N3 is in 2.8 Angstrom of 2-RES.N3
***The following residues are in the Metal Site:
Residue 1-PT
Residue 2-RES
***The large model contains the following residues:
[1, 2]
I check the standard.fingerprint file, and found N1 N2 N3 are assigned as
X1 X2 X3 respectively while cl is still cl.
In this way if I continue the following steps, at last I'm afraid the bond
between Cl and Pt cannot be generated(I'm not quite sure).
I attach my file for your reference.
Do you have any suggestion?
Your kind help will be highly appreciated!
2016-07-01 23:54 GMT+08:00 Pengfei Li <ambermailpengfei.gmail.com>:
> 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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing list
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Sincerely,
Mr. Meng Zhenyu
Division of Chemistry and Biological Chemistry
School of Physical and Mathematical Sciences
Nanyang Technological University
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- application/octet-stream attachment: RES.mol2
- application/octet-stream attachment: PT.mol2
Received on Sat Jul 02 2016 - 07:00:03 PDT
