Describe the bug AutoDock Vina v1.2.3 has no '--log' option To Reproduce execution of https://mmb.irbbarcelona.org/biobb/workflows/tutorials/vs_ebi, "Running the Docking" section Expected behavior vina --ligand prep_ligand.pdbqt --receptor prep_receptor.pdbqt --center_x=23.913 --center_...
in Vina, the degrees of freedom that only move hydrogens, such as the hydroxyl group torsions, aredegenerate.Therefore, in the output,some hydrogen atoms can be expected to be positioned randomly(but consistent
I've downloaded the mac os file "vina_1.2.3_mac_x86_64" and put it into a folder on my mac. I've set the Autodock Vina to run as a local file and pointed Chimera to the file I downloaded, but when I try to run it I get an error; "vina_1.2.3_mac_x86_64" is not an ...
AutoDock(英)
以Autodock-Vina为例。 PTGS2.pdb:原始的受体蛋白,包含了这个晶体自带的配体。 PTGS2.pdbqt:受体蛋白,经过处理从PDB转化成PDBQT格式wend。 Paeonol.pdbqt:小分子,我是利用Open Babel直接从MOL2格式转成PDBQT格式。 Paeonol.zip:Windows下,利用PaDEL-ADV对接运行完成后,产生的对接结果压缩文档。
AutoDock Vina provides faster docking predictions, while Attracting Cavities offers more accurate results. Ligands can be imported in various ways, including as files, SMILES notation or molecular sketches. Targets can be imported as PDB files or identified by their PDB ID. In addition, advanced ...
Part2: commandine procedure ref:AutoDock Vina: Molecular docking program 1.prepare receptor and ligand with pymol-open-source, adding hydrogen. pymol-open-source install with anaconda (test in python=3.8): conda install -c conda-forge pymol-open-source(work for win and linux) 2. use ...
C:\Program Files\MGLTools-1.5.6\lib\site-packages\AutoDockTools\autoanalyzeCommands.py", line ...
使用基于AutoDock Vina的优化版本对接软件Smina 进行含有小分子的蛋白靶点的验证自我对接,以及与未知结合模式的小分子的预测对接。可携带口袋水分子进行对接。 - 飞桨AI Studio
估计就是这个原因。格点计算autogrid，计算时间就是很短，几秒就结束，不过它会显示进程，当时间消失就...