[Dock-fans] Docking with metal ions

Scott Brozell sbrozell at rci.rutgers.edu
Tue Jan 24 00:26:34 PST 2012


Hi,

On Thu, Jan 19, 2012 at 11:12:05AM +0100, Jose R. Valverde wrote:
> 	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.

Yes, it will be interesting to read whether the atoms flagged
with the inv_a error are Mg.
Note that the conventional wisdom is that bare ions should
not be used with GB.

> 	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? 

Mg is in the Dock Amber Score ions library;
dock6/parameters/leap/cmd/leaprc.dock.ions
This is automatically processed and definitely works for
MG in the receptor.  Be sure to use the name MG.
Note that the model here is Mg as a bare divalent cation.
If you are having problems with MG in the ligand then 
send me an example input file and I'll investigate.

scott



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