Input Files for the Absolute Binding Enthalpies of BRD4-1 and Ligand Complexes

The input files provided in this dataset are used to run molecular dynamics simulations of BRD4-1 and ligand complexes for absolute binding enthalpies and binding free energies. We evaluated the performance of absolute enthalpy of binding calculations for ten inhibitors against a member of the bromodomain family, BRD4-1, against isothermal titration calorimetry data. 

The input files include the following:

1. Enthalpy_inputs.zip (Absolute binding enthalpy calculation); These input files are for 4 sets of simulations including complex, apo-receptor, ligand and pure water simulations. a) The topology files for the definitions of the molecules. b) The force field files for the parameters. c) The coordinate files (solv.gro) for the initial coordinates of the atoms in the system. d) The simulation parameter files (mdp files) for the simulation settings, such as the time step, temperature, pressure, etc.

2. ABFE_inputs.zip (Absolute binding free energy calculation); a) The topology files for the definitions of the molecules. b) The force field files for the parameters. c) The coordinate file (gro files for ZA1 and ZA2) which contains the initial coordinates of the atoms in the system. d) The simulation parameter files (mdp files) of each window (coul, restraint and vdw) for the simulation settings, such as the time step, temperature, pressure, etc. 

3. ligand-parameters-topologies.zip; The topology and force field files for all ligands.