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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.
*

*>
*

I 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

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:

I 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 _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amber _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Fri Dec 16 2016 - 08:00:02 PST

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