Re: [AMBER] pka of CYS

From: Carlos Simmerling <carlos.simmerling.gmail.com>
Date: Tue, 13 Dec 2016 14:27:36 -0500

thanks Jason.
CYM is not part of the database for ff14SB.
carlos

On Tue, Dec 13, 2016 at 1:55 PM, Jason Swails <jason.swails.gmail.com>
wrote:

> On Tue, Dec 13, 2016 at 1:22 PM, Carlos Simmerling <
> carlos.simmerling.gmail.com> wrote:
>
> > Ok that's good, my point was that the standard force field parameters
> don't
> > include the negatively charged Cys so they would need to be somewhere for
> > this to work. I'm glad the cph people added these in. It might be good to
> > add Cys- to the standard parameter set if its commonly used.
> >
>
> ‚ÄčI believe CYM is the negatively-charged cysteine residue you're referring
> to, and that's the charge set that was used for the deprotonated state of
> CYS.
>
> The 3 synonyms are CYX (no proton, neutral charge for disulfides), CYS
> (protonated cysteine), and CYM (deprotonated cysteine).
>
> All the best,
> Jason
>
> --
> Jason M. Swails
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Received on Tue Dec 13 2016 - 11:30:02 PST
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