Re: [AMBER] pka of CYS

From: Sowmya Indrakumar <soemya.kemi.dtu.dk>
Date: Fri, 16 Dec 2016 15:33:28 +0000

Can someone kidnly help me resolve this issue?

I have now completed constph MD run, gone uptil pH = 9. Using cphsats on *.cpout files, I could generate files containing predicted pka values (as shown in tutorials 18).

For, pH from 0 to 9: predicted pKa for CYS is always *inf, can anybody tell me what the issue is? (see below the output file)

Solvent pH is 9.000
CYS 4 : Offset inf Pred inf Frac Prot 1.000 Transitions 0
AS4 9 : Offset -3.824 Pred 5.176 Frac Prot 0.000 Transitions 14
GL4 10 : Offset -2.432 Pred 6.568 Frac Prot 0.004 Transitions 253
AS4 11 : Offset -4.456 Pred 4.544 Frac Prot 0.000 Transitions 6
AS4 12 : Offset -4.187 Pred 4.813 Frac Prot 0.000 Transitions 6
CYS 15 : Offset inf Pred inf Frac Prot 1.000 Transitions 0
HIP 16 : Offset -3.721 Pred 5.279 Frac Prot 0.000 Transitions 76
HIP 18 : Offset -2.773 Pred 6.227 Frac Prot 0.002 Transitions 662
CYS 19 : Offset inf Pred inf Frac Prot 1.000 Transitions 0
CYS 30 : Offset inf Pred inf Frac Prot 1.000 Transitions 0
CYS 37 : Offset inf Pred inf Frac Prot 1.000 Transitions 0
CYS 39 : Offset inf Pred inf Frac Prot 1.000 Transitions 0

Average total molecular protonation: 8.006

I look forward for suggestions.
Regards
Sowmya
________________________________________
From: Jason Swails [jason.swails.gmail.com]
Sent: Tuesday, December 13, 2016 7:55 PM
To: AMBER Mailing List
Subject: Re: [AMBER] pka of CYS

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 Fri Dec 16 2016 - 08:00:02 PST
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