PDB2ENTROPY and PDB2TRENT: Conformational and Translational–Rotational Entropy from Molecular Ensembles

• DOI: 10.1021/acs.jcim.8b00143
• Publication Date: 2018-06-13T14:37:07Z
• Authors: Federico Fogolari; Ornela Maloku; Cedrix Jurgal Don...; Alessandra Corazza; Gennaro Esposito
• Keywords: Models, Molecular; Rotation; Entropy; Molecular Conformation; Benzene; 01 natural sciences; 0103 physical sciences; Solvents; Computer Simulation; Muramidase; Molecular Conformation; Rotational and conformational entropy; Computer Simulation; free energy, entropy, molecular dynamics simulations, rotation-translation; Software

Entropy calculation is an important step in the postprocessing of molecular dynamics trajectories or predictive models. In recent years nearest neighbor method has emerged as a powerful to deal flexible way with dimensionality problem. Here we provide two programs, PBD2ENTROPY and PDB2TRENT that compute conformational translational–rotational entropy, respectively, based on method. PDB2ENTROPY takes input files containing following: (1) ensembles same molecule(s) PDB format (2) definitions torsion angles (a default file provided where additional user can be easily implemented). samples complexed molecules, string specifying atoms providing reference framework superimpose samples, used rotation translation one molecule respect other. The C programs sample demonstration data are available GitHub repository (URL: http://github.com/federico-fogolari/pdb2entropy http://github.com/federico-fogolari/pdb2trent).