"Methodological and force field effects in the molecular dynamics-based prediction of binding free energies of host-guest systems"

Dataset for reproducing ADFEs for host-guest systems with ORAC6.1ORAC6.1 can be downloaded form www1.chim.unifi.it/orac 

Directory tree .├── bin├── SP6│   ├── HREM_ions_job│   │   └── b-RSTRT│   ├── HREM_job│   │   └── b-RSTRT│   ├── lib│   ├── NE_Alchemy_ions_job│   │   └── u_ions-RSTRT│   ├── NE_Alchemy_job│   │   └── u-RSTRT│   ├── pdb│   ├── rem_start│   ├── traj│   └── work_data├── templates├── w└── WP6    ├── docking    ├── HREM_job    │   └── b-RSTRT    ├── lib    ├── NE_Alchemy_job    │   └── u-RSTRT    ├── pdb    ├── rem_start    ├── traj    └── work_data

 SP6/WP6: contains data for WP6 host guest system      see SP6[WP6]/README file for more explanations 

      HREM_job [HREM_ions_job]: directory containing the input files      for preparing and running the HREM stage

      NE_Alchemy_job [NE_Alchemy_ions_job]: directory for preparing and running      the NE alchemical stage stage

 lib:  contains ORAC GAFF tpgprm files pdb:  contains the PDB guest and host files docking:  contains the starting Vina-generated structures for the complex work_data:  contains the work files for the bound and unbound NE alchemy bin: contains ancillary scripts for pre- and post-processing data traj: contain HREM-generated pdb trajectories for the bound state and apo WP6 w: contains equilibrated structure for OPC3 water templates: input templates used by scripts to produce input files            for selected guest/host systems