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 - 08:30:02 PDT
