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
Received on Tue Mar 12 2019 - 07:30:02 PDT
