Dear pengfei,
No the ligand has not covalent bonds with the dna is the cyclen-Cu(II) -
h2o system which i don't know how to treat.
The copper is coordinated by the nitrogen's in the cyclen ring and the
water, and it's key in the dna catalysis, i just want to study the Dynamics
of the docked system for specific distances and angle that allow catalysis
Thanks a lot
Fabian
On Sat, Mar 16, 2019, 17:19 Pengfei Li <ambermailpengfei.gmail.com> wrote:
> 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
> >
> > _______________________________________________
> > 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
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Apr 05 2019 - 22:00:02 PDT
