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GA后做PLIP(加cu)
cu的相互作用小分子的相互作用CU的相互作用小分子的相互作用原创 2022-07-08 15:14:31 · 349 阅读 · 1 评论 -
2021-1-5
File: src/core/chemical/ResidueTypeSetCache.cc:106[ ERROR ] UtilityExitExceptionERROR: Error in core::chemical::ResidueTypeSetCache::add_residue_type(): Attempting to add a new residue type, but residue type '00C' already exists in the cache. (Did you l原创 2021-01-05 17:16:52 · 254 阅读 · 0 评论 -
vHTS注意事项
运行生成js文件的命令与前面的数据库和flag.txt以及xml无关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原创 2021-01-05 16:25:36 · 222 阅读 · 0 评论 -
用一个小分子一个蛋白质运行vHTS
利用教程一的小分子ETQ和蛋白质3PBL_A_ETQ.pdbunbuntu@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.csv0 records processedunbuntu@unbuntu-vir原创 2021-01-05 09:45:06 · 164 阅读 · 1 评论 -
vHTS(js)
{ "jobs": [ { "proteins": [ "protein_files/1KV2_cleaned_0001.pdb", "protein_files/1KV2_cleaned_0002.pdb" ], "ligands": [ "ligand_files/params/ac/AU.pdb", "ligand_files/params/a9/AF.pdb", "ligand_files/params/bc/AN.pdb",原创 2021-01-04 15:22:52 · 184 阅读 · 0 评论 -
对接命令
$ mpirun -np 6 /home/unbuntu/rosetta_src_2019.35.60890_bundle/main/source/bin/rosetta_scripts.mpi.linuxgccrelease @inputs/options -docking:ligand:ligand_ensemble 0 -nstruct 500 $ mpirun -np 6 /home/unbuntu/rosetta_src_2019.35.60890_bundle/main/source/bin原创 2020-12-01 19:07:24 · 168 阅读 · 0 评论 -
1hzy_Funclib:XML
<ROSETTASCRIPTS>Dock the ensemble of ligand into the native structure using the Rosetta Score based affinities <SCOREFXNS> <ScoreFunction name="ligand_soft_rep" weights="ligand_soft_rep"> <Reweight scoretype="fa_elec" weight="0原创 2020-12-01 18:10:36 · 156 阅读 · 0 评论 -
Funclib:1hzy对接
unbuntu@unbuntu-virtual-machine:~/ligand_docking/3_Ensemble_docking$ $ROSETTA/main/source/scripts/python/public/molfile_to_params.py prep/make_params/make_params.GD.sdf --chain F -n 00F -p 00F --conformers-in-one-fileCentering ligands at ( 2.000, 0.0原创 2020-11-30 10:49:23 · 196 阅读 · 0 评论 -
error:AFFINITY does not exist in ResidueType with name 00B
在生成的params.pdb中最后一行添加NUMERIC_PROPERTY AFFINITY 0运行成功原创 2020-11-27 11:37:52 · 65 阅读 · 0 评论 -
model_aliganed蛋白与NTBC、HPPA、sulco、mesot小分子结合体对接:error not exist 00B
1、(1)生成小分子NTBC的conformers文件D:\bcl_4.0>bcl.exe molecule:ConformerGenerator -ensemble_filenames NTBC.sdf -conformers_single_file NTBC.conformers.sdf(2)生成小分子sulcotrione的conformers文件D:\bcl_4.0>bcl.exe molecule:ConformerGenerator -ensemble_filenames原创 2020-11-26 17:15:43 · 216 阅读 · 0 评论 -
vHTS
1、flag.txt中-parser:script_vars startfrom=/home/unbuntu/ligand_docking/2_vHTS/protein_files/1kv2_startfrom.pdb/1kv2_startfrom.pdb没有在job_01.js的蛋白中设置路径,添加这个蛋白的路径运行unbuntu@unbuntu-virtual-machine:~/ligand_docking/2_vHTS$ /home/unbuntu/rosetta_src_2019.35.60原创 2020-11-23 14:10:31 · 219 阅读 · 0 评论 -
vHTS
1、用ligand_fileds下的job_01.js把params文件内容添加全路径unbuntu@unbuntu-virtual-machine:~/ligand_docking/2_vHTS$ /home/unbuntu/rosetta_src_2019.35.60890_bundle/main/source/bin/rosetta_scripts.default.linuxgccrelease @ flags.txt -in:file:screening_job_file ligand_file原创 2020-11-19 17:37:35 · 291 阅读 · 0 评论 -
运行vHTS
把1KV2蛋白质生成conformers文件D:\bcl_4.0>bcl.exe molecule:ConformerGenerator -ensemble_filenames 1KV2_Validation_Affinities_3D.sdf -conformers_single_file 1KV2_Validation_Affinities_3D.conformers.sdfunbuntu@unbuntu-virtual-machine:~/ligand_docking/2_vHTS$ /h原创 2020-11-18 19:46:56 · 252 阅读 · 0 评论 -
pycharm安装pandas超时解决
原创 2020-11-14 17:43:35 · 696 阅读 · 0 评论 -
numpy1
shape数组类型原创 2020-11-14 17:41:33 · 44 阅读 · 0 评论 -
编译mpi
下面的代码仅使用5个内核编译MPI格式和发布模式的rosetta_scripts应用程序:> ./scons.py -j 5 mode=release bin/rosetta_scripts.mpi.linuxgccrelease extras=mpi编译失败打开unbuntu–>Application Launcher -->Applications–>(搜索新立得)Synaptic Package–>(搜索)Clang–>(mark)clang、libClang-原创 2020-11-11 15:37:37 · 448 阅读 · 0 评论 -
做4pud等蛋白的箱线图
#coding utf-8import numpy as npfrom matplotlib import pyplot as pltarray1 = np.array([-14.105,-14.101,-12.135,-12.023,-11.897])array2 = np.array([-8.733,-8.607,-7.892,-7.834,-7.682])array3 = np.array([-11.559,-11.457,-11.441,-11.27,-10.305])m1 = np原创 2020-11-11 14:49:23 · 196 阅读 · 0 评论 -
编译mpi
unbuntu@unbuntu-virtual-machine:~/rosetta_src_2019.35.60890_bundle/main/source$ ./scons.py -j 5 mode=release bin/rosetta_scripts.mpi.linuxgccrelease extras=mpiscons: Reading SConscript files ...Running versioning script ... Release package detected, usi原创 2020-11-10 17:44:39 · 268 阅读 · 1 评论 -
2020-10-27:option -qsar:grid_dir is not set.
进行对接报错,添加上运行成功将box-size="5.0"改为50,运行一下命令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 ..原创 2020-10-29 09:51:59 · 111 阅读 · 0 评论 -
2020-10-24蛋白质和小分子对接成功笔记
D:\bcl_4.0>bcl.exe molecule:ConformerGenerator -ensemble_filenames HBT.sdf -conformers_single_file HBT.conformers.sdfD:\bcl_4.0>bcl.exe molecule:ConformerGenerator -ensemble_filenames HBT.sdf -conformers_single_file HBT.conformers.sdfD:\bcl_4.0>原创 2020-10-24 21:50:27 · 1058 阅读 · 0 评论 -
10.15笔记:下载小分子文件
unbuntu@unbuntu-virtual-machine:~/test$ /home/unbuntu/rosetta_src_2019.35.60890_bundle/tools/protein_tools/scripts/clean_pdb.py 4pud Abcl.exe molecule:ConformerGenerator -ensemble_filenames prep/aligned_ligands/4AGL.withH.sdf \ -conformers_single_fi原创 2020-10-21 20:31:41 · 353 阅读 · 0 评论 -
2020.10.21笔记:参考教程三对O-pnp.sdf做分子对接(Error)
(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conformer原创 2020-10-21 20:30:50 · 472 阅读 · 0 评论 -
10.16笔记:O-PNPX2.sdf分子对接
(1) bcl.exe molecule:ConformerGenerator -ensemble_filenames O-PNPX2.sdf -conformers_single_file O-PNPX2.sdf#chain="C",步骤2的chain要与它保持一致,链C为自己定义,也可以是其它<StartFrom name="start_from" chain="C"> <Coordinates x="103.673" y="31.99原创 2020-10-21 20:32:18 · 112 阅读 · 0 评论