Hello,
You should look at the original paper by Mongan, et. al. (2004). He
defines carboxylates to have 4 titratable protons -- one in the syn- and
anti- position of each oxygen atom, since the proton can be in any of those
states. I would argue that you _need_ 2 of them, since it can be on either
oxygen. Adding the additional 2 (so you have 2 syn- and 2 anti- oxygens
available) helps convergence because it ensures that no titrating proton
will get "stuck" in the anti- position and resist re-protonation.
Also part of the model is the idea that hydrogen atoms are "added" and
"removed" simply by adjusting partial charges. A GL4 (or AS4) is
"deprotonated" when all 4 of its hydrogen atoms have a charge of 0 and the
remaining atoms have a net charge of -1. They are protonated when a
_single_ hydrogen has a non-zero net charge (the other 3 hydrogens _still_
have a charge of 0), and the whole residue has a net charge of 0.
As for CYS residues -- I believe AmberTools 1.5 defines a titratable CYS
residue (a protonated cysteine). However, there is no mechanism for
de-forming a cystine disulfide bond in constant pH MD (as Professor Case
mentioned), nor is there any prescription for defining titratable termini.
HTH,
Jason
On Tue, Feb 21, 2012 at 8:57 AM, Ngo Son Tung <nstung.ifpan.edu.pl> wrote:
> Dear Prof. Case,
>
> Thanks for your reply, but how about GLU (or GL4)?
>
> Regards,
>
> Son Tung
>
> > On Tue, Feb 21, 2012, Ngo Son Tung wrote:
> >>
> >> I want to run simulation in constant pH with impicit solvent for Insulin
> >> protein at pH 1.6. I used AmberTool version 1.4 (included in Ambermd 11)
> >> make topology for this protein. I changed GLU to GL4, HIS to HIP ...
> >> (follow Amber11 manual).
> >> H
> >> |
> >> I found GLU become: R-C-O(+)-H
> >> |
> >> (+)O-H
> >> | H H
> >> H | |
> >> and disulfate make by two CYS become: R-S(+)-S(+)-R
> >
> > I don't think you want this doubly protonated disulfide. I suspect(?)
> > that
> > you used CYS as the residue name, and may have used the "bond" command to
> > add
> > the S-S bond (or maybe not---you can see why it's often hard to reply
> when
> > people say things like "I followed the Amber manual"). I'm not sure I
> > know
> > what really happens to disulfide bonds at low pH, but I am (pretty) sure
> > that
> > Amber has no parameters to describe such a situation. Make the cysteine
> > residues CYX (not CYS), and then add the S-S bond using the "bond"
> > command.
> >
> > Constant pH calculations are an advanced subject. Start with the easiest
> > case
> > you can think of, maybe even with only one residue having variable
> > protonation, and make sure you understand what is going on. Then move on
> > to
> > more complex situations.
> >
> > ....dac
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
> --
> Son Tung Ngo
>
>
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Tue Feb 21 2012 - 20:30:02 PST
