"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 ORAC6.1
ORAC6.1 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