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

[Maik Goette]

Hi

Depends on your system, but in principle yes.
A Cystein should be neutral. If you take a deprotonated one to build a 
complex with the zinc, it should be neutral afterwards.

Lets assume a case with HIS/HIS/CYS as complex partners. the resdiues 
without a complex are assumed to be neutral. Therefore, their charges 
added should be 0. Add your zinc to the complex, take a partial charge 
of 0.7xx for it and modify the charges of the complex partners (i.e. the 
S and in the case of histidine it makes sense to spread the charge 
difference over the ring). If you now add up all the charges of all 
complex partners, the system should again be at charge 0.
I can't see the problems, sorry.

Regards

Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
37077 Goettingen
Germany
Tel.  : ++49 551 201 2310
Fax   : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
         mgoette2[at]gwdg.de
WWW   : http://www.mpibpc.gwdg.de/groups/grubmueller/


raja wrote:
> 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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