title: Alchemical Free Energy Estimators and Molecular Dynamics Engines: Accuracy, Precision and Reproducibility
author: Wade, Alexander
description: This zip contains all input structures for paper the: Alchemical Free Energy Estimators and Molecular Dynamics Engines: Accuracy, Precision and Reproducibility Authors: Alexander D. Wade, Agastya P. Bhati, Shunzhou Wan, Peter V.Coveney The structures of the folders are protein/ligand_transformation/alchemical_leg/input/files The ligand transformation are derived from previous work by wang et al. (https://pubs.acs.org/doi/10.1021/ja512751q) There are two files for the solvent alchemical leg: complex.pdb and complex.prmtop complex.pdb is  structure file that also denotes the alchemical atoms in the pdb beta column. complex.prmtop is an AMBER parameter/topology file For the complex alchemical leg there is an additional file constraints.pdb that contains the constraint information in the pdb beta column. These files can be used with TIES_MD (https://ucl-ccs.github.io/TIES_MD/) or other molecular dynamics engiens that take AMBER input.