it depends a little on which protein force field you are using. I am not
aware of deprotonated Thr parameters for ff14SB, which is the most recent
force field from my group. Others may be able to say something about other
force fields. The ff14SB manuscript has extensive supporting information
that provides all of the details needed to add new amino acids that will be
compatible.
CS
On Thu, Mar 24, 2016 at 12:03 PM, anu chandra <anu80125.gmail.com> wrote:
> Dear Amber users,
>
> I am working with a metalloprotein where the metals ion is coordinated with
> oxygen (gamma oxygen) atom of threonine residue. In order to preserve this
> interaction during simulation, I would like to keep the threonine in its
> deprotonated stage. So, I just wonder whether Amber forcefield have
> parameters are available for deprotonated threonine?. If not, how can one
> derive the Amber compatible parameters for a deprotonated threonine?
>
> Many thanks in advance
> Anu
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Received on Thu Mar 24 2016 - 09:30:06 PDT
