This is the supporting material of the paper:
"A nonequilibrium alchemical method for drug-receptor absolute binding free energy calculations: application to the bromodomain testbed"
Maurice Karrenbrock, Piero Procacci, Francesco Luigi Gervasio

Here one can find the starting conformations used in the paper for the protein ligand complex, the ligand in vacuum, and the ligand in water (only lig 1 to 6).
The crystallographic conformations are the same used in the paper: http://dx.doi.org/10.1039/C5SC02678D with the only difference being that we had to add one dummy atom on the center of mass of the protein because of how the pulling algorithm in gromacs deals with periodic boundary conditions. For the case of ligand 11 that has 2 configurations in the orgininal paper, we used only one of them (the first one).
The docked conformations of ligand 6, 7, and 8 have been obtained with autodock, and are therefore not the same as the ones in the paper http://dx.doi.org/10.1039/C5SC02678D .

The topology files are the same used in http://dx.doi.org/10.1039/C5SC02678D .
For ligand 6, 7, and 8 also the TOP files with re-parametrized dihedrals with ANI-2.X forcefield are given.

Also the MDP files used are given


Most of the pre and post processing has been done with HPC_Drug-v2.0 https://github.com/MauriceKarrenbrock/HPC_Drug/
For the rest there are the scripts in the bin/ directory

Each directory contains a README.txt with more detailed information

Structure of this directory:

├── bin/ = scripts
├── lib/ = topology files
├── etc/ = license files and other
├── gro_pdb/ = structure files
├── HREM/ = replica exchange
├── NE/ = alchemical transformations
└── README.txt

