Re: [AMBER] cPHMD: how to define residues with two pkas

From: Cruzeiro,Vinicius Wilian D <>
Date: Thu, 3 Sep 2020 03:28:41 +0000

This is possible. Take a look at what is done for the residue HIP.

Vinícius Wilian D Cruzeiro

PhD Candidate
Department of Chemistry, Physical Chemistry Division
University of Florida, United States

Voice: +1(352)846-1633<tel:+1(352)846-1633>

On Sep 2, 2020, at 7:36 PM, Kolattukudy P. Santo <> wrote:

[External Email]

Hello all

I want to define/parameterize a non standard residue with two
carboxylic groups, having different pkas for each group's protonation.
Is it possible to define in AMBER, a titratable residue with multiple
protonation sites having different pkas, such as pka1, pka2 ?
I can see that there are residues with multiple protonation states (like
PRN) defined, but all states have the same pka.

Thank you

KP Santo
Dr. Kolattukudy P. Santo
Post doctoral Associate
Department of Chemical and Biochemical Engineering
Rutgers, The State University of New Jersey
New Brunswick, New jersey
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Received on Wed Sep 02 2020 - 21:00:02 PDT
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