usage: prepare_input.py [-h] --p_in P_IN --p_out P_OUT --l_in L_IN --l_out L_OUT
optional arguments:
-h, --help show this help message and exit
--p_in P_IN protein input; PDB format
--p_out P_OUT protein output; PDB format
--l_in L_IN ligand input; SDF format
--l_out L_OUT ligand output; SDF format
usage: main.py [-h] [-p P] [-l L] [-c C] [-t T] [-s] [-o O] [-v]
optional arguments:
-h, --help show this help message and exit
-p P protein_fn in PDB format
-l L ligand_fn in SDF format
-c C complex_fn in PDB format
-t T traj_fn in DCD format
-s solvate system with water
-o O log_fn
-v verbose
usage: analyze_rmsd.py [-h] -t T -c C
optional arguments:
-h, --help show this help message and exit
-t T trajectory file; DCD format
-c C system topology file; PDB format