Rotational Profiler: A Fast, Automated, and Interactive Server to Derive Torsional Dihedral Potentials for Classical Molecular Simulations

• DOI: 10.1021/acs.jcim.0c01168
• Publication Date: 2020-11-20T06:00:36Z
• Authors: Victor H. Rusu; Denys E. S. Santos; Marcelo D. Poleto; Marcelo M. Galheigo; Antônio T. A. Gomes; Hugo Verli; Thereza A. Soares; Roberto D. Lins
• Keywords: 0301 basic medicine; 03 medical and health sciences; Computers; Least-Squares Analysis; Algorithms

Rotational Profiler provides an analytical algorithm to compute sets of classical torsional dihedral parameters by fitting an empirical energy profile to a reference one that can be obtained experimentally or by quantum-mechanical methods. The resulting profiles are compatible with the functional forms in the most widely used biomolecular force fields (e.g., GROMOS, AMBER, OPLS, and CHARMM). The linear least-squares regression method is used to generate sets of parameters that best satisfy the fitting. Rotational Profiler is free to use, analytical, and force field/package independent. The formalism is herein described, and its usage, in an interactive and automated manner, is made available as a Web server at http://rotprof.lncc.br.