Re: [AMBER] Suspicious pKas from CpHMD

From: Matthew Guberman-Pfeffer via AMBER <>
Date: Thu, 9 Feb 2023 06:36:21 +0000

Hi Vinicius,

Thanks for your quick reply. Your suggestion was very informative! The output showed me that the protonated fraction for Lys-8 and AS4-114 is always >0.99 and <0.005, respectively. So, the pKas are strange because only extremely rare transitions are being sampled.

What are the lowest and highest extremes in pH you’d recommend testing? Is it 2 to 12 (the pKas range, I think can be measured in aqueous solutions)?


From: Vinicius Wilian Cruzeiro <>
Date: Thursday, February 9, 2023 at 12:58 AM
To: <>, Matthew Guberman-Pfeffer <>
Subject: Re: Suspicious pKas from CpHMD
*Message sent from a system outside of UConn.*

Hello Matthew,

You should take a look at the fractions of protonated species as a function of pH for these residues. This will give you an idea on why you are getting these fitted values.

One possibility is that you are having a conformational change and then your fractions of protonated species vs pH will not have a nice sigmoidal shape, what could explain the fitted values you got.

Also, I would not exclude the possibility that you need to add more pH values, as you pointed out. Notice that the plots I am suggesting will tell you if this is what you need to do.

I hope this helps,

Vinícius Wilian D. Cruzeiro, PhD
Postdoctoral Researcher
Department of Chemistry
Stanford University
Twitter: .vwcruzeiro
From: Matthew Guberman-Pfeffer via AMBER <>
Sent: Wednesday, February 8, 2023 9:08 PM
To: <>
Subject: [AMBER] Suspicious pKas from CpHMD

Dear AMBER Community,

I’m getting some really strange pKas for CpHMD simulations performed at pHs from 5 to 10. For example,

LYS 8: pKa = 564.07106 (+- 9292.89711 ) ; Hill coefficient = 0.004 (+- 0.060 )
AS4 114: pKa = -52.65171 (+- 144.03991 ) ; Hill coefficient = 0.046 (+- 0.112 )

Each simulation was propagated for 40 ns. My CpH-relevant settings were icnstph=2, ntcnstph=100, ntrelax=100, and solvph = 5, 6, 7, 8, 9, or 10.

Is there anything besides running the simulations for longer that I should try? Should I expand the range of considered pHs? What else can I try to get more reasonable pKas for these residues? Or, what should I inspect to see if something is going wrong?


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Received on Wed Feb 08 2023 - 23:00:03 PST
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