#!/bin/bash
export OMP_THREAD_LIMIT=18

# Arg1 is a protein number like 01
# Arg2 is a ligand name like 1OIU-N76

vina_1.2.5_win.exe --receptor p$1_receptor.pdbqt --ligand testlig-$2.pdbqt --config known_box.txt --exhaustiveness=32 --num_modes 20 --seed -337841744 --out p$1_$2_vina_out.pdbqt >& p$1_$2_vina-log

C:/Users/ann/.conda/envs/my-rdkit-env/Scripts/mk_export.py p$1_$2_vina_out.pdbqt -o p$1_$2_vina_dock.sdf

# Convert to mol2
obabel p$1_$2_vina_dock.sdf -O p$1_$2_vina_dock.mol2

surflex-dock-v5190-win64.exe rms_list p$1_$2_vina_dock.mol2 gold-$2.mol2 rms-p$1-$2

