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Saturday, February 17, 2018

get_conformations.py: a simple script to generate rotamers



Here's a simple script for generating rotamers. It assumes the input geometry is reasonable and perturbs the dihedral angles of n rotateable bonds by \pm 120^\circ. It makes all 3^n combinations of dihedral angles but if that is larger than a user-defined cutoff it will pick a random subset. Rotateable bonds include alcohol, phenols, and primary amines, but also amide bonds.  It doesn't know about equivalent atoms, so it will happily rotate a tert-butyl or trifluoromethyl group.



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