@WAMM
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# 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/homeyer/tutorial/structs
multi_structure_lig_file      
output_path                  /home/homeyer/tutorial
rec_structure                /home/homeyer/tutorial/input_info/2RA0_IN.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                 1

# Request structure separation
# structure_separation: Separate ligands specified in one multi-structure
#                       input file and generate one structure file per ligand.
structure_separation         0

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# Creation of LEaP input files
#
# prepare_leap_input: Generate files for LEaP input
# non_neutral_ligands: Total charge of at least one molecule is not zero.
#                      In this case the total charge of each non-neutral
#                      molecule must be defined in lig_charge_file.
# lig_charge_file: File with information about total charges of ligands.
# am1_lig_charges: Calculate AM1-BCC charges.
# resp_lig_charges: Calculate RESP charges. In this case charges must be
#                   computed with the program Gaussian in an intermediate step.
#                   Batch scripts for Gaussian calculations will be prepared
#                   automatically, if requested (see prepare_gauss_batch_file
#                   and gauss_batch_template below).
# calc_charges: Calculate charges according to requested procedure.
#               If this flag is set to zero, no atomic charges are calculated.
# resp_setup_step1: Step 1 of RESP charge calculation: Preparation of
#                   Gaussian input.
# resp_setup_step2: Step 2 of RESP charge calculation: Generation of LEaP input
#                   from Gaussian output.
# prepare_gauss_batch_file: Generate batch script for Gaussian input if RESP
#                           charge calculation is performed. A batch template
#                           file (gauss_batch_template) is required.
# gauss_batch_template: Batch template file
#                       Prerequisite: resp_lig_charges=1, resp_setup_step1=1
#                       and prepare_gauss_batch_file=1
# gauss_batch_path: Basic working directory for Gaussian jobs
# average_charges: If the charges of two steroisomers shall be averaged, so that
#                  both ligands obtain the same atomic charges, a file in which
#                  the stereoisomer pairs are specified must be given here.
prepare_leap_input           1
non_neutral_ligands          0
lig_charge_file              
am1_lig_charges              1
resp_lig_charges             0
calc_charges                 1
resp_setup_step1             0
resp_setup_step2             0
prepare_gauss_batch_file     0
gauss_batch_template          
gauss_batch_path              
average_charges