Hello Santo,
Yes, it is possible to run constant pH MD for non-standard residues. I suggest you to take a look at section 22.5 of the Amber 2019 manual that talks specifically about that.
I hope this helps,
All the best,
Vinícius Wilian D. Cruzeiro
PhD Candidate
Department of Chemistry, Physical Chemistry Division
University of Florida, United States
Voice: +1(352)846-1633
________________________________
From: Kolattukudy P. Santo <santotheophys.gmail.com>
Sent: Friday, August 30, 2019 12:00 PM
To: AMBER Mailing List <amber.ambermd.org>
Subject: [AMBER] Constant PH simulations for non-proteins and nonstandard residues
Hi
I want to run simulations with ph changes. I see that it is possible for
proteins from AMBER advanced Tutorials. Is possible to run it for any
nonstandard molecules in solution?
Santo
--
*Dr. K. 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 Fri Aug 30 2019 - 11:30:02 PDT
