[Dock-fans] Docking with metal ions

Jose R. Valverde jrvalverde at cnb.csic.es
Thu Jan 19 02:12:05 PST 2012


Dear all,

	besides the problems in my previous message, I am also trying
to dock a molecule that is normally associated with a metal ion. My
problem is how to get Zou GB/SA scores or estimate binding affinity.

	The problem is that the ion should be placed wherever the ligand
docks, i. e. always relative to the ligand pose, as it is not normally
coupled to the enzyme, but the ligand. So docking should be done with
the ion included in the ligand.

	I do get the primary conformers using a grid score, but when
they are minimized and rescored with Zou GB/SA I keep getting weird 
results (likely due to the presence of Mg++ in the ligand). Although
I do not get these errors with Hawkins GB/SA or PB/SA, I'm worried
the results may be wrong as well.

	Something similar happens with Amber score: I cannot generate
a topology for the ligand+ion (I tried SwissParam, ATB,..) and
so the Amber method refuses to work.

	Can anybody suggest any good alternative approach? 

				j
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