#! /usr/bin/env python # -*- coding: utf-8 -*- # # My first example with AutoDock Vina in python # from vina import Vina # 导入Vina包 v = Vina(sf_name='vina') # 指定进行分子对接的力场:Vina ; 如果你想使用AutoDock4或Vinardo力场,请将vina换成ad4或vinardo v.set_receptor('1iep...
相关的研究成果以 “AutoDock Vina 1.2.0: New Docking Methods, Expanded Force Field, and Python Bindings” 为题发布在国际著名期刊Journal of Chemical Information and Modeling上。 1.评分函数扩展和改进 一个主要的改进是Vina中AD4评分函数的可用性。它允许用户使用相同的基于Vina MC的搜索算法访问它,并以同...
$ pythonsh /your/path/AutoDock-Vina-1.2.2/example/autodock_scripts/prepare_gpf.py -l 1iep_ligand.pdbqt -r 1fpu_receptor_rigid.pdbqt -y 其中, -y指定的是将配体在盒子中自动居中,如果配体和受体蛋白的结构不能很好的叠合,则需要添加-p gridcenter='X,X,X'手动定义盒子中心。 即可得到1fpu_recept...
在Autodock vina 运行结束后,会生成多个结果文件,包括得分最低的配体对应的 pdbqt 文件和配体与受体的交互信息文件(interaction file)等。可以通过读取这些文件来提取 Autodock vina 的结果并进行解析。 以下是 Python 代码示例: #读取 pdbqt 文件 with open('output.pdbqt', 'r') as f: lines = f.readlines(...
利用python实现Autodock Vina多对多分子对接结果筛选并绘制热图 (0)踩踩(0) 所需:7积分 Vue开发学习路径目录大纲.md 2024-11-14 17:43:47 积分:1 WeTalk 2024-11-14 17:40:59 积分:1 七夕节微信表白墙小程序源码/基于Laravel的表白墙微信小程序源码 ...
As part of a script I am writing, I need to install the package autodock vina for the purpose of ligand and protein binding. Every time I attempt to "pip install vina", I recieve an error message " ValueError: Boost library location was not found!". Upon attempting to install boost...
I am writing a python script and encountered with a following error: ... v = vina.Vina(sf_name='ad4', verbosity=1, seed=selectedSeed) ... v.set_receptor(rigid_pdbqt_filename=="xxx.pdbqt",flex_pdbqt_filename="yyy.pdbqt") ... ERROR: Only f...
Here, we describe the implementation of this functionality in AutoDock Vina 1.2.0. Additionally, AutoDock Vina 1.2.0 supports the AutoDock4.2 scoring function, simultaneous docking of multiple ligands, and a batch mode for docking a large number of ligands. Furthermore, we implemented Python ...
在vina的tutorial里,你需要安装ADFR套装,在linux下它有.app安装包,很容易,以后要用到里边的prepare_ligand.py和prepare_receptor.py两个python文件。 4,其它安装选项 tutorial里说可以用pip安装 命令如下: 代码语言:javascript 复制 $ conda create-n vina python=3$ conda activate vina ...
Hello, I was trying to rigid dock with ad4 scoring function on python script. The tutorial seems like that by changing scoring function's name, it is possible to use ad4 with rigid docking However, it gave the error from vina import Vina...