Hello Madhusmita,
It is possible, but you need to know the pKa of these groups in a reference compound. You can find instructions on how to parametrize your system for CpHMD simulations in section 26.5 of the Amber22 manual.
I hope this helps,
Vinícius Wilian D. Cruzeiro, PhD
Postdoctoral Researcher
Department of Chemistry
Stanford University
Twitter: .vwcruzeiro
________________________________
From: MADHUSMITA DEVI via AMBER <amber.ambermd.org>
Sent: Tuesday, March 7, 2023 10:33 AM
To: amber.ambermd.org <amber.ambermd.org>
Subject: [AMBER] Constant pH MD simulation of non-protein systems
Dear Amber Users,
I have a non-protein system consisting of titratable groups, -OH and -NR2. I wished to know if CpHMD simulation is possible for such groups in non-protein systems. If yes, kindly guide me through it or provide any suitable tutorial for the same.
Thank you in advance.
Madhusmita Devi
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Received on Tue Mar 07 2023 - 11:00:03 PST
