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
>
>
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--
Son Tung Ngo
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Received on Tue Feb 21 2012 - 06:00:02 PST
