（1）
#在此目录下生成conformers文件 D:\bcl_4.0>bcl.exe molecule:ConformerGenerator -ensemble_filenames 4AGL.withH.pdb -conformers_single_file 4AGL.conformers.pdb（2）将生成的conformers文件传到unbuntu教程三prep/conformers目录下 （3）
#生成make_params.4AGL.sdf文件，运行这一步下一步时才能生成conformers.pdb文件 unbuntu@unbuntu-virtual-machine:~/ligand_docking/3_Ensemble_docking$ cat prep/aligned_ligands/4AGL.withH.sdf prep/conformers/4AGL.conformers.sdf >> prep/make_params/make_params.4AGL.sdf（4）
#修改了dock.xml中chain="B,C,E,F"-->chain="B" unbuntu@unbuntu-virtual-machine:~/ligand_docking/3_Ensemble_docking$ /home/unbuntu/rosetta_src_2019.35.60890_bundle/main/source/bin/rosetta_scripts.linuxgccrelease @inputs/options -docking:ligand:ligand_ensemble 0 -nstruct 1 protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "transform_ensemble" of type TransformEnsemble Error: [ ERROR ] ERROR: Exception caught by JobDistributor while trying to get pose from job 'protein_ligands_0001' Error: [ ERROR ] Treating failure as bad input; canceling similar jobs [ ERROR ]: Caught exception: File: src/core/chemical/ResidueType.cc:2718 AFFINITY does not exist in ResidueType with name 00B #将dock.xml中chain="B,C,D,E,F"修改回来后，运行成功，生成score.sc文件以及B_1,C_1,D_1,F_1,E_1.pdb文件以及protein_ligands_0001.pdb文件（protein_ligands为options中-in -file的文件即分子和蛋白质文件） unbuntu@unbuntu-virtual-machine:~/ligand_docking/3_Ensemble_docking$ /home/unbuntu/rosetta_src_2019.35.60890_bundle/main/source/bin/rosetta_scripts.linuxgccrelease @inputs/options -docking:ligand:ligand_ensemble 0 -nstruct 1 protocols.rosetta_scripts.ParsedProtocol: setting status to success protocols.jd2.JobDistributor: protein_ligands_0001 reported success in 23 seconds protocols.jd2.JobDistributor: no more batches to process... protocols.jd2.JobDistributor: 1 jobs considered, 1 jobs attempted in 23 seconds将教程三与4AGH.pdb不相干的文件全部删除，依旧运行成功，生成以下文件：
1、参照教程三的文件命名及格式运行test报错（错误同上） 2、在test中生成了00B,00C…等小分子文件并合并成一个ligands.pdb文件放入inputs文件中做小分子的对接（与教程三的小分子文件保持一致），运行报错。 3、比较教程三与test的不同，发现test的蛋白质文件比教程三的蛋白质文件少一些数据。
