[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’ 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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