Alchemical Free Energy Estimators and Molecular Dynamics Engines: Accuracy, Precision and Reproducibility

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.