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

[raja]

Dear Mark,
Thanks for your reply. Well, I have well taken your point of making
separate charge group constituting Zn and its residues and I am working
out for it, in mean time I need some clarification in my present
approach.

I just detailed out my earlier mail hereunder.  I am using AMBER force
field.

This is default partial charge distribution for deprotonated Cystine
 CYM      N     -0.4157      
 CYM      H      0.2719      
 CYM     CA     -0.0351      
 CYM     HA      0.0508      
 CYM     CB     -0.2413      
 CYM    HB1      0.1122      
 CYM    HB2      0.1122      
 CYM     SG     -0.8844      
 CYM      C      0.5973     
 CYM      O     -0.5679         
------------------------
Formal Charge = -1.00000
----------------------------

Now my modified partial charge at SG to -0.6944

 CYM      N     -0.4157      
 CYM      H      0.2719      
 CYM     CA     -0.0351      
 CYM     HA      0.0508      
 CYM     CB     -0.2413      
 CYM    HB1      0.1122      
 CYM    HB2      0.1122      
 CYM     SG     -0.6944      
 CYM      C      0.5973     
 CYM      O     -0.5679         
------------------------
Formal Charge = -0.8100
-----------------------

According to manual, to ensure integer value of total charge on the
residue CYM (cysteine). Ideally, following the force field convention, I
would like to do readjustment of the individual partial charges to make
it as total =  -1. But on other hand this is my intuition that, formal
charge for -1 for CYM is applicable for free Cysteine residue in AMBER
force field, but in my case, it is harmonically bonded with zinc and
also the charge transfer is taken place. This makes me to think that the
formal charge of CYM should be adjusted to neutral. Please give your
thought?

With thanks !
B.Nataraj











On Tue, 28 Nov 2006 17:51:04 +1100, "Mark Abraham"
<Mark.Abraham at anu.edu.au> said:
> 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&#8217; 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.
> 
> Mark
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-- 
  raja
  raja_28 at fastmail.us

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