AutoDock-Vina

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Variability in docking scores across multiple runs with the same predicted pose

5

Hello, I am wondering why I am seeing variability in docking scores across multiple runs. I have 1000 structures that I have docked a single ligand to, saved the first...

bnovakborna

How to install MolKit for flexible docking using script prepare_flexreceptor.py?

2

I'm following the Flexible Docking tutorial found here: [https://autodock-vina.readthedocs.io/en/latest/docking_flexible.html](https://autodock-vina.readthedocs.io/en/latest/docking_flexible.html) on an AWS ubuntu instance. When I try to run the **prepare_flexreceptor.py** script I get an import error. However, I can't...

emilyrkang

compile in macOS chip M1

2

some error I install brew install gcc boost try to make get this error ` >>>make aarch64-apple-darwin21-g++-11 -static -pthread -ansi -Wno-long-long -O3 -DNDEBUG -std=c++11 -DVERSION=\"v1.2.3-3-gd913876-mod\" -I /opt/homebrew/Cellar/boost/1.76.0/include -I ../../../src/lib -o...

hotwa

Failed to load grid map - python script

1

Hello. I tried to run Vina with the grid maps using the python script, but it seems that the grid maps were not loaded. I was working at "AutoDock-Vina-1.2.3/example/python_scripting". **First...

nimijkrap

Hi, I'm trying to compile Vina on CentOS 7 (centos-release-7-9.2009.1.el7.centos.x86_64) kernel (3.10.0-1160.49.1.el7.x86_64). I have compiled boost in /opt/boost ``` tar -xzf boost_1_* cd boost_1_*/ ./bootstrap.sh --prefix=/opt/boost ./b2 install --prefix=/opt/boost --with=all...

chuckisbusy

Error when try install with pip command

1

Hi, I'm trying to install Vina but when I use the command `pip install -U numpy vina` I get this, but I can´t understand the error: ``` Collecting vina Using...

deeplearchem

Hydrated Docking - Dry.py error

5

All, I am following the directions in Autodock Vina Read the Docs on hydrated docking. I am able to reproduce all steps except the post-processing using dry.py. I can split...

jfair32

about covalent docking

2

is it possible to perform covalent docking with vina 1.2.3 and covalent docking based virtual screening (batch file mode)? can I install this tool (vina 1.2.3) in windows ?

debanjansen48

Vina API multiple ligand docking, showing no conformation generation

1

Hello, I am trying to use Vina's API for multi-ligand docking, but it fails. I try as follows: 1. Add pdbqt ligand twice 2. Write to a line to add...

SynchronyML

Python script: Rigid docking with AD4 Scoring Function

5

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...

kimnupjuk