jixing475 / Schrodinger-Script

Some scripts to run Schrödinger jobs on HPC or localhost.

Schrodinger-Script

Scripts to run Schrödinger jobs.

Scripts

Linux shell scripts (Vsgo GVSrun plmd DSMDrun XDock) to run Virual Screening, Molecular Dynamics Simulation in Schrodinger. Using -h option to show help information for this scripts, such as GVSrun -h.

   GVSrun or Vsgo: Virual Screening;

   plmd or DSMDrun: Molecular Dynamics Simulation;

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

GVSrun and plmd is higher recommoned than Vsgo and DSMDrun.

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 necessary for GVSrun, Vsgo and XDock;

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

3:Desmond (installation path of Schrodinger or Academic Desmond) is necessary for plmd and DSMDrun;

4: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 Desmond=/public/home/wanglin3/software/DS21

How to cite

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

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