@WAMM ################################################################################ # Location and features of input and output directories / file(s) # # lig_struct_path: Folder containing the ligand input file(s) # multi_structure_lig_file: Basename of ligand file, if multi-structure # file is provided # output_path: Basis directory in which all setup and analysis # folders will be generated # rec_structure: Receptor structure in PDB format # bound_rec_structure: Optional, alternative receptor structure in bound # conformation to be used for 3-trajectory approach lig_struct_path /home/local/soemya-loc/site_1_WT/structs multi_structure_lig_file output_path /home/local/soemya-loc/site_1_WT rec_structure /home/local/soemya-loc/site_1_WT/receptor.pdb bound_rec_structure # Specification of ligand input format lig_format_sdf 0 lig_format_mol2 1 # Receptor features # water_in_rec: Water present in receptor PDB structure water_in_rec 0 ################################################################################ # Setup of molecular dynamics simulations # # setup_MDsimulations: Perform setup of simulation input # traj_setup_method: 1 = One trajectory approach # 3 = Three trajectory approach # MD_am1: Prepare simulations with AM1-BCC charges # MD_resp: Prepare simulations with RESP charges # SSbond_file: File with disulfide bridge definitions # additional_library: If an additional library file is required, e.g. for # non-standard residues present in the receptor structure, # this file must be specified here. # additional_frcmod: If additional parameters are needed, e.g. for describing # non-standard residues present in the receptor structure, # a parameter file should be provided here. # MD_batch_path: Path to basis directory in which the simulations shall # be performed in case this differs from . # If no path is given, it is assumed that the path is # equal to # MDequil_template_folder: Path to directory with equilibration template files # total_MDequil_time: Total equilibration time in ps # MDequil_batch_template: Batch template file for equilibration # MDprod_template: Template file for production phase of MD simulation # total_MDprod_time: Number of ns to simulate # MDprod_batch_template: Batch template file for MD production # no_of_rec_residues: Number of residues in receptor structure # restart_file_for_MDprod: Base name of restart-file from equilibration that # shall be used for production input setup_MDsimulations 1 traj_setup_method 3 MD_am1 1 MD_resp 0 SSbond_file /home/local/soemya-loc/site_1_WT/disulfide_bridges.txt additional_library /home/local/soemya-loc/site_1_WT/CA.lib additional_frcmod MD_batch_path MDequil_template_folder /home/local/soemya-loc/site_1_WT/equi total_MDequil_time 400 MDequil_batch_template /home/local/soemya-loc/site_1_WT/equi.pbs MDprod_template /home/local/soemya-loc/site_1_WT/MD_prod.in total_MDprod_time 2 MDprod_batch_template /home/local/soemya-loc/site_1_WT/prod.pbs no_of_rec_residues 40 restart_file_for_MDprod md_nvt_red_06 backward = 1