Hello Prof. Carlos,
Thanks for the reply. I will be using Amber ff14SB force field. As you
suggested, I will look into the manuscript for information about adding new
parameter.
Anu
On Thu, Mar 24, 2016 at 9:44 PM, Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> 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 - 15:30:02 PDT
