Re: [AMBER] pka of CYS

From: Jason Swails <>
Date: Tue, 13 Dec 2016 13:55:55 -0500

On Tue, Dec 13, 2016 at 1:22 PM, Carlos Simmerling <> 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

The 3 synonyms are CYX (no proton, neutral charge for disulfides), CYS
(protonated cysteine), and CYM (deprotonated cysteine).

All the best,

Jason M. Swails
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Received on Tue Dec 13 2016 - 11:00:03 PST
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