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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Received on Tue Feb 21 2012 - 05:30:04 PST
