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

From: Kolattukudy P. Santo <santotheophys.gmail.com>
Date: Wed, 2 Sep 2020 22:35:40 -0400

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 

-- 
Best,
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
USA
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Received on Wed Sep 02 2020 - 20:00:02 PDT
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