Dear amber experts,
I am willing to run MD for a protein gyrase, pdb 2xkk, which has four MG+2
atoms in the catalytic center coordinated by 2 waters and asp acids. I
notice that in the advanced tutorial 20 there is a bonded and a non-bonded
methodology to obtain metal parameters, prepare a lib, etc, which one I
should use for Mg+2 ??
Additionally, to make things more complicated, I am docking a cyclen-Cu(II)
based ligands on this target, which also I would then like to run MD on the
docked complex. 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 and Mg ions in
this case??
Any comments, pointers or ideas or source of information will be more than
appreciated.
Thanks in advance!
*Best,FabianFabian Glaser PhDHead of the Structural Bioinformatics
section Bioinformatics Knowledge Unit - BKUThe Lorry I.
Lokey Interdisciplinary Center for Life Sciences and EngineeringTechnion -
Israel Institute of Technology, Haifa, IsraelWeb
http://bku.technion.ac.il/
<
http://bku.technion.ac.il/>Tel +972 (0) 4 8293701*
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Received on Tue Mar 12 2019 - 09:30:02 PDT
