Hi,
Many thanks for your help.
Regards,
Son Tung
> 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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>>
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
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>
--
Son Tung Ngo
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Received on Wed Feb 22 2012 - 08:00:02 PST
