[AMBER] Benzene ring planarity

From: Intravaia, Lauren E via AMBER <amber.ambermd.org>
Date: Mon, 1 Apr 2024 19:28:23 +0000

Hello,

I am performing MD simulations of enzyme-inhibitor complexes using AMBER ff19sb forcefield. I noticed that benzene rings on the small molecular do not remain planar throughout the simulation. I derived forcefield parameters after geometry optimization and ESP calculation with gaussian. Is there anything I can do to maintain planarity of the planar rings during the simulation?

Thank you,
Lauren

--
Lauren Intravaia
PhD Candidate
Lab of Dr. Celia Schiffer
Dept. of Biochemistry and Molecular Biotechnology
University of Massachusetts Chan Medical School
364 Plantation St. LRB 970D
Email: lauren.intravaia.umassmed.edu<mailto:lauren.intravaia.umassmed.edu>
Website: https://www.umassmed.edu/schifferlab/
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Received on Mon Apr 01 2024 - 12:30:02 PDT