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)
分子对接2d图用Autodock-Vina分析。 在开始蛋白-分子的互作分析前,我们当然需要一个蛋白-分子结合文件图,即一个PDB文件。通常,在使用软件完成蛋白-分子对接后,我就能利用对应的软件去提取蛋白-分子结合的文件,即PDB文件。不同的软件有不同的方法。 以Autodock-Vina为例。
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 ...
Autodock vina 和MGL tools linux版本操作(命令行操作) 蛋白质Edit——加polar Hautodock vina,加Kollman电荷后,Grid——Macromolecule——choose,自动保存pro1.pdbqt 配体Ligand——Input——QuickSetup,自动保存.out.pdbqt receptor = clusters_0001_model1.pdbqt ...
用AutoDock Vina或DOCK 6真香，开源的，可以发文章，而且计算比较准确。就安装比较麻烦。不过网上有个...
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 ...
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 ...