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

raja raja_28 at fastmail.us
Tue Nov 28 14:24:11 CET 2006


Thanks Goette for your mail. So system neutrality is restored as per
your advice but individual residue will deviate from its integer value
(formal charge), won’t violate anything? I remember once I read the
lines of individual residues' partial charge should be an integer from
gromacs manual, I really took some time to search it in manual to refer
that line in this mail, but I could not find it. But I am also using
Autodock (Docking tool), where the non-integral charge on residue based
is not allowed. May be I overlapped these two programs concept of
partial charges!

By,
B.Nataraj
 

 the desired partial charge 
On Tue, 28 Nov 2006 11:48:40 +0100, "Maik Goette"
<mgoette at mpi-bpc.mpg.de> said:
> 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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-- 
  raja
  raja_28 at fastmail.us

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