Hi Fabian,
so I understand you want to parameterize a complex of Cu (II), to simulate
with a protein.
If you obtained the substrate protein system through molecular docking, and
the ligand is not covalently bound to some atom of the protein, you can try
to parametrize the complex first as program MCPB.py (being one of the
authors Pengfei Li), first and then join the files to obtain the final
topology of the complex system.
If your substrate protein system has covalent bonding, you must first
parameterize the metal center using, for example, the MCPB.py program
Best
Em sáb, 16 de mar de 2019 12:19, Pengfei Li <ambermailpengfei.gmail.com>
escreveu:
> Hi Fabian,
>
> For the Mg2+ ions, a nonbonded model is suggested due to the ionic nature
> of Mg2+.
>
> For the Cu2+ ion, I am not sure I understand your question correctly or
> not. So you have a cyclen-Cu(II) system as a ligand, and does this ligand
> have covalent bond with the protein?
>
> -Pengfei
>
> > On Mar 12, 2019, at 10:00 AM, Fabian Glaser <fabian.glaser.gmail.com>
> wrote:
> >
> > Dear amber experts,
> >
> > OK, so here comes one that may trivial for most, but not for me…
> >
> > I am willing to run MD for a protein gyrase, pdb 2xkk, which has four
> MG+2 atoms in the catalytic center surrounded by water and asp acids. I
> notice that in the advanced tutorial 20 there is a bonded and a non-bonded
> model methodology, which one I should use for Mg+2 ??
> >
> > Additionally, to make things more complicated, I am using a
> cyclen-Cu(II) system ligand based for docking on this target, which also I
> would like to run MD on the docked complex, so I will need also to
> parametrize the ligand Cu+2 bonded to this ligand. So the same question
> here, how should I prepare the Cu+2 in this case??
> >
> > And comments, pointers or ideas or source of information will be more
> than appreciated.
> >
> > Thanks in advance!
> >
> > Best,
> >
> > Fabian
> >
> > Fabian Glaser PhD
> >
> > Head of the Structural Bioinformatics section
> > Bioinformatics Knowledge Unit - BKU
> > The Lorry I. Lokey Interdisciplinary Center for Life Sciences and
> Engineering
> > Technion - Israel Institute of Technology, Haifa, Israel
> > Web http://bku.technion.ac.il/
> > Tel +972 (0) 4 8293701
> >
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Received on Sat Mar 16 2019 - 09:00:02 PDT
