scrub.py mols.smi -o mols.sdf
mkdir mols_pdbqt
mk_prepare_ligand.py -i mols.sdf --multimol_outdir mols_pdbqt
With autodock-gpu
mkdir vs_adgpu
/disk/diogom/code/AutoDock-GPU/bin/autodock_gpu_128wi -B mols_pdbqt -M rec_3oxz_rot315_rigid.maps.fld -F rec_3oxz_rot315_flex.pdbqt -N vs_adgpu -C 1
Or With vina
mkdir vs_vina
~/vina_1.2.5_linux_x86_64 --scoring ad4 --maps rec_3oxz_rot315_rigid --flex rec_3oxz_rot315_flex.pdbqt --batch ../scrub/ligs_2/*.pdbqt --dir vs_vina/
Use ringtail script to assemble results into sqlite database file
rt_process_vs.py write -o vs_adgpu.db -fp vs_adgpu/
With vina, we tell it to add interactions (-ai) with the receptor file (-rf)
rt_process_vs.py write -o vs_vina.db -fp vs_vina/ -m vina -ai -rf rec_3oxz_rot315_rigid.pdbqt
For the next step, we will use a .db file that contains AutoDock-GPU results.