Hello Kankana,
Thank you for your interest in this methodology.
I recommend the following resources to get started with the C(pH,E)MD methodology: this Amber tutorial ( https://ambermd.org/tutorials/advanced/tutorial33/index.php ) and this paper ( https://pubs.aip.org/aip/jcp/article/149/7/072338/1075419/Redox-potential-replica-exchange-molecular ).
All the best,
Vinícius Wilian D. Cruzeiro, PhD
Scientist II, Computational Chemistry
Architect Therapeutics
Twitter: .vwcruzeiro
________________________________
From: Kankana Bhattacharjee via AMBER <amber.ambermd.org>
Sent: Monday, April 1, 2024 11:35 PM
To: AMBER Mailing List <amber.ambermd.org>
Subject: [AMBER] Regarding constant pH and redox potential simulation:
Dear AMBER users,
I am trying to use amber constant pH and redox potential simulation.To
build up the prmtop and inpcrd files should I have to follow the
conventional procedure using tleap module ya I have to follow the
tleap-explicit.in or tleap-implicit.in. Also, modules for constant pH and
redox potentials are bit different. Like, leaprc. constph and leaprc.conste
modules. So,have to load these modules for performing constant pH and redox
potential simulation ?
Kindly help me with this.
Thanks & Regards
Kankana Bhattacharjee
Ph.D. Scholar
Department of Chemistry
Ashoka University
Sonipat, Haryana
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Received on Tue Apr 02 2024 - 14:30:02 PDT
