docking-org/zinc22-3d

Repository for scripts relating to the dock3 ligand pipeline- the creation of db2 files.

3D Building Pipeline

This code will generate db2 files from smiles/mol2.

Required Software

• CORINA
• Openeye OMEGA (code is setup to use the openeye python toolkit, could be reworked to use command line version)
• Chemaxon JCHEM (cxcalc and molconvert)
• Openbabel
• Anaconda (Miniconda 3)

Getting Started

1. Fork this repository
2. Clone directory, cd into created directory
3. Run install.sh
4. Install conda to either a shared nfs path or the '/soft' directory
5. Create the conda environment using 'conda env create -f environment.yml -n envname'
6. Move required software to '/soft' directory. Software must be .tar.gz format
7. Move required licenses to '/licenses' directory (Jchem/Omega). Software looks for jchem-license.cxl and oe-license.txt by default. These can be changed in the env.sh files
8. Change paths in env.sh file (required changes are lines that are commented out)
9. Modify the 'submit/build-3d.bash' file, source the conda environment on the first line

Running The Pipeline

1. Source the conda environment
2. Set optional/required environment variables (see here)
3. Run 'bash submit/submit-all.bash' to start job