Re: [AMBER] Deprotonation of Tyr using Parmed

From: Jason Swails <jason.swails.gmail.com>
Date: Mon, 28 Aug 2017 21:57:59 -0400

On Thu, Aug 24, 2017 at 9:04 AM, Sowmya Indrakumar <soemya.kemi.dtu.dk>
wrote:

> Hi Jason,
> Thanks for the comments. I am following you're tutorial of constant pH MD
> in explicit solvent. Since the saltconc=0.1, how would I go about doing it
> at a different salt concentration? In that case, reference energies should
> be defined at that concentration?
>

‚ÄčThe salt concentration here is for the GB protonation state changes only.
You are unlikely to notice any real effect from modifying that parameter.
That said, if the model for salt effects is physically accurate, reference
energies should not need to be recalculated I don't think. The calculated
pKa will be different, but real pKas are dependent on the ionic strength of
the solution, too. Which comes back to my statement -- as far as the salt
effect modeling is accurate, so too will the calculated pKa shift as a
result of ionic strength differences.

That said, I don't know that I trust the GB screening model of the ionic
strength that well.

Good luck,
Jason

-- 
Jason M. Swails
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Received on Mon Aug 28 2017 - 19:00:04 PDT
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