1）用CPU的话，Vina 1.2.5就足够。打分函数能用AD4、Vina等，搜索算法也比AD4好[AutoDock Vina 1...
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 --recept...
$ conda activate vina $ conda install -c conda-forge numpy openbabel $ pip install meeko 操作步骤 本教程以Autodock Vina 1.2.2安装包中自带的例子“FDA认证的抗癌药物imatinib与c-Abl 蛋白进行对接(PDB ID: 1IEP)”作为介绍对象(具体路径:/your/pathway/AutoDock-Vina-1.2.2/example/basic_docking/solut...
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 add...
水合Docking方法有一定的发展,已经在AutoDock4中应用,而目前该对接方法通过修改力场的方式模拟显式的水桥分子,嵌入到AutoDock Vina 1.2.x版本中,这无疑对Vina用户是一个利好消息。从AutoDock Vina官方的测评介绍中可以看出,对比于基础Docking方法,水合Docking方法预测片段尺寸分子结合构象的准确性有明显提高,因此该方法...
You can change the weights easily, by specifying them in the configuration file, or in the command line. For example vina --weight_hydrogen -1.2 ... doubles the strenth of all hydrogen bonds. Functionality that would allow the users to create new atom and pseudo-atom types, and specify th...
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 Vina does not provide a graphical user interface, but fortunately the command line entry is straightforward. 23. Save the file vina_1.2.3_windows_x86_64.exe. We will use the following path C:\Program Files (x86)\Vina_1_2_3, i.e., create a folder named Vina_1_2_3 under ...
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。