1_initial_structure ligands - XYZ files: Initial structures of the ligands - m1.com: Example of geometry optimization - esp_m1.com: Example of ESP charges calculation - m1.pdbqt: Example of pdbqt file receptor - 7zub.pdb: PDB from Protein Data Bank of PDB ID:7ZUB - pasb.pdb: PDB of chain D of 7ZUB protein - pasb.pdbqt: pdbqt of chain D of 7ZUB protein membrane - DOPC_128.pdb: PDB file of the relaxed membrane structure 2_docking(protein) - conf.txt: Input for docking 3_MD protein - 1_min.in: Minimization - 2_equil.in: Heating - 3_prod.in: Production - system_m*.crd and system_m*.parm7: coordinates and parameter for each system membrane - min.in: Minimization - heat.in: Heating - prod_*.in: Production - pull.in: Pulling - DOPC_m*.pdb and DOPC_m*.prmtop: coordinates and parameters for each system 4_MMGBSA(protein) - contact.in: cpptraj input to search the contacts between the ligand and the receptor - mmgbsa.in: MMGBSA input to calculate the binding free energy, its decomposition and the contribution per residue for the residues with higher contact 5_umbrella_sampling(membrane) - prod_window.in: Window production example - COM_dist.RST: Window parameter file - full_fe_m*.dat: Free energy curve for each system 6_EDA - main.inp and tpl.inp: inputs for MoBioTools - complex_geom0.com, mon1_geom0.com and mon2_geom0.com: Created inputs from MoBioTools to run single points on Gaussian16 - input: input for EDA-NCI - EDA_m*_memb.dat: Data file with the EDA results on the selected sample for the membrane system - EDA_m*_prot.dat: Data file with the EDA results on the selected sample for the protein system