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Rotational Profiler: A Fast, Automated, and Interactive Server to Derive Torsional Dihedral Potentials for Classical
Victor H Rusu1, Denys E S Santos2, Marcelo D Poleto3
1Swiss National Supercomputing Centre, Lugano, Ticino 6900, Switzerland.
Abstract:
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.
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