[gmx-users] Partial charge distribution for metal ligating atoms

Mark Abraham Mark.Abraham at anu.edu.au
Tue Nov 28 07:51:04 CET 2006

raja wrote:
> Hi gmxions,
> There are many references, say that Zn2+ partial charge should be
> reduced to ~0.7 rather than the force field default value of 2. In line
> with that there are many values published for distributed charge in its
> surrounding ligand atoms in compensation for loss of positive charge of
> Zn.

OK, so this strategy preserves charge neutrality over the zinc and a 
bunch of ligand residues. It will not preserve charge neutrality of the 
individual residues, obviously.

> Now I am having set of values to be distributed for my system's
> active site residues, say for one SG-Cys, and two NE2-His atoms. My
> question is that what will be net formal charge for these residues after
> its specific atoms' charges are modified. 

The old value, plus the modification?

> In other words, for example,
> after modifying default partial charge of SG-Cys from  -0.8844 to
> -0.6944, Should I adjust its net formal charge to -1 or to 0? 

Not sure where you're adjusting the "net formal charge" or why you think 
it's necessary.

What you really want to do is have charge groups with integral values of 
charge (see section 3.4.2 and some part of Chapter 5 for how to do 
this), so that probably means combining the zinc with chunks of these 
residues into one large +2 charge group.

> Then on
> what basis I can adjust rest of the atoms’ partial charges.

Why would you do this? Whatever you do should be consistent with the 
most reliable scheme in the literature, unless you want to create an 
expensive random number generator.


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