用一个小分子一个蛋白质运行vHTS_materials studio小分子和蛋白-优快云博客

本文链接：https://blog.youkuaiyun.com/qq_39212193/article/details/112212589

利用教程一的小分子ETQ和蛋白质3PBL_A_ETQ.pdb

unbuntu@unbuntu-virtual-machine:~/ligand_docking/2_vHTS$ $ROSETTA/tools/hts_tools/sdf_split_organize.py ligand_files/ETQ_conformers.pdb ligand_files/split_conformers/ ligand_names.csv
0 records processed

在这里插入图片描述

unbuntu@unbuntu-virtual-machine:~/ligand_docking/2_vHTS$ $ROSETTA/tools/hts_tools/sdf_split_organize.py ligand_files/ETQ_conformers.pdb ligand_files/split_conformers/ ligand_names.csv
0 records processed
unbuntu@unbuntu-virtual-machine:~/ligand_docking/2_vHTS$ $ROSETTA/tools/hts_tools/setup_screening_project.py ligand_names.csv ligand_db.db3                   
unbuntu@unbuntu-virtual-machine:~/ligand_docking/2_vHTS$ $ROSETTA/tools/hts_tools/add_activity_tags_to_database.py ligand_db.db3 ligand_activities.csv
skippped 52
unbuntu@unbuntu-virtual-machine:~/ligand_docking/2_vHTS$ $ROSETTA/tools/hts_tools/make_params.py -j 5 --database /home/unbuntu/rosetta_src_2019.35.60890_bundle/main/database/ --path_to_params /home/unbuntu/rosetta_src_2019.35.60890_bundle/main/source/scripts/python/public/molfile_to_params.py ligand_db.db3 ligand_files/params/
Traceback (most recent call last):
  File "/home/unbuntu/rosetta_src_2019.35.60890_bundle/tools/hts_tools/make_params.py", line 210, in <module>
    add_ligand_names(file_information,options.database)
  File "/home/unbuntu/rosetta_src_2019.35.60890_bundle/tools/hts_tools/make_params.py", line 149, in add_ligand_names
    name_size = required_ligand_name_length(len(ligand_path_data))
  File "/home/unbuntu/rosetta_src_2019.35.60890_bundle/tools/hts_tools/make_params.py", line 64, in required_ligand_name_length
    return max(2,int(ceil(log(ligand_count)/log(character_space))))
ValueError: math domain error

把教程一的ETQ.params、ETQ.pdb、

unbuntu@unbuntu-virtual-machine:~/ligand_docking/2_vHTS$ python2.7 /home/unbuntu/rosetta_src_2019.35.60890_bundle/tools/hts_tools/make_evenly_grouped_jobs.py ligand_files/params/ protein_files/ --n_chunks 1 --max_per_job 1000 --inactive_cross_dock job
ERROR: ligand_files/params/ contains no params files