Re: [AMBER] pka of CYS

From: Eric Lang <eric.lang.bristol.ac.uk>
Date: Fri, 16 Dec 2016 15:59:11 +0000

Hi,

The pKa is 'inf', because no transitions between protonated and
deprotonated states have occurred so there is no way the pKa can be
predicted.
Perhaps you can try to run your simulations at a higher pH.

Eric

On 16 December 2016 at 15:33, Sowmya Indrakumar <soemya.kemi.dtu.dk> wrote:

> 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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>



-- 
Eric Lang
BrisSynBio Postdoctoral Research Associate Modelling
Centre for Computational Chemistry
School of Chemistry - University of Bristol
Bristol BS8 1TS - United Kingdom
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Received on Fri Dec 16 2016 - 08:00:02 PST
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