Hello Nathan,
Take a look at section 26.5 of the Amber21 manual for information on how you can parametrize and setup constant pH MD for additional titratable residues. AmberTools has specific scripts to help with this process.
I hope this helps,
All the best,
Vinícius Wilian D. Cruzeiro, PhD
Postdoctoral Researcher
Department of Chemistry
Stanford University
Twitter: .vwcruzeiro
________________________________
From: Nathan Black <nathanblack262.gmail.com>
Sent: Monday, March 7, 2022 8:36 PM
To: AMBER Mailing List <amber.ambermd.org>
Subject: [AMBER] Constant pH MD Simulations for General Organic Compounds
Hello AMBER Users,
I have been reading the AMBER 20 manual regarding the use of constant-pH
molecular dynamics. From using the --list command for cpinutil.py, I am
under the impression that its use is intended exclusively for certain amino
acid and nucleic acid residues.
If I wanted to run an MD simulation containing molecules that do *not *have
supported residues (such as organic counterions or drugs with ionizable
groups), would my best bet be to run normal MD with the molecules set to
their most probable protonation state(s) based upon their known pKa values? Are
there external resources that would make constant-pH simulations possible
for such broad applications?
All the best,
-NDB
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Received on Mon Mar 07 2022 - 21:00:03 PST
