CADD-Scripts (using Schrödinger and Rosetta)

Scripts to run Schrödinger and Rosetta jobs.

News

• 2025/04/02, we add an option -u to control the strain energy correction. The default is false, this may result in GVSrun's behavior being different from before.

Installation

Download CADD-Scripts and set the environment variable.

git clone https://github.com/Wang-Lin-boop/CADD-Scripts
cd CADD-Scripts
echo "export PATH=${PWD}:\${PATH}" >> ~/.bashrc
chmod +x XDock
chmod +x GVSrun
chmod +x ProteinMC
source ~/.bashrc

Scripts

Linux shell scripts (XDock, GVSrun, ProteinMC) to run Virual Screening, Cross-Docking and MC Simulations. Using -h option to show help information for this scripts, such as GVSrun -h.

   GVSrun: Virual Screening;

   XDock: Reverse Docking, Global Docking and Batch Grid Genenation.

   ProteinMC: Protein Relax, Protein-Protein Docking, MM-GBSA Calculation. 

Related-Script

Refer to AutoMD for automated execution of molecular dynamics simulations and trajectory analysis.

Chinese documents

中文文档可以访问：

XDock

靶标垂钓

GVSrun and plmd

Environment Variables

These environmental variables are necessary:

1:SCHRODINGER (installation path of Schrodinger) is required for GVSrun, and XDock;

2:compound_library (compound library for your compound databases) is required for GVSrun;

3:rosetta_app or rosetta_db (installation path of rosetta) is optional for XDock;

You can add those Environment Variables to your ~/.bashrc!

For example, export SCHRODINGER=/public/home/wanglin3/software/SCHRODINGER

How to cite

It is recommended that citing the script by a link (such as: GVSrun(https://github.com/Wang-Lin-boop/CADD-Scripts)) or refer to this page Ways to cite a GitHub Repo to promote reproducibility of your work.