[AMBER] Reference energies in CpHMD (constant pH MD) for HIP

From: Rodrigo Pérez Cossio <rodrigoperez93.hotmail.com>
Date: Fri, 22 Feb 2019 00:16:48 +0000


I wonder if I understand it right.

Let's say we want to parametrize again HIP reference energies and test the new energies.
We have HIP, HID (pKa 6.5), and HIE (pKa 7.1).

If we run a CpHMD with the right reference energies, we should obtain:
1) At pH 6.5, the protonation fraction at D position is 50%. Then, the fractions should be: HIP+HID = HIE
2) At pH 7.1, the protonation fraction at E position is 50%. Then, the fractions should be: HIP+HIE = HID

Is this correct?

Thank you in advance!

Rodrigo Cossio Pérez
Universidad Nacional de Quilmes
Buenos Aires, Argentina

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Received on Thu Feb 21 2019 - 16:30:03 PST
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