ZINC22:Building 3D

Redirect to:

• Building The 3D Pipeline ZINC22

This describes how to become a contributor to ZINC-22

Step 1. Download DOCK.3.8 and other software

• Note: DOCK.3.8 has a lot of software in it, which can make it a bit expensive to throw in a software image.
• When 3D building, only a small portion of the DOCK software is used, so at the lab we have a "stripped down" version of DOCK for 3d building.
• You can find this version at /nfs/home/xyz/soft/DOCK.3.8.0.3d.tar.gz and also at files.docking.org/private/software/DOCK.3.8.0.3d.tar.gz.

Ask chemistry4biology at gmail dot com for credentials

• Download python3 environment (lig_build_py3-3.7.1.tar.gz)
• Download Jchem 19.15 (jchem-19.15.tar.gz)
• Download Corina (supply your own corina executable, name the folder it resides in corina, tar that folder up into corina.tar.gz)
• Download Libraries (lib.tar.gz)
• Clone submission scripts to somewhere you can use them. (https://github.com/btingle/zinc-3d-build-3.git)

• All tar.gz can be found in /nfs/home/xyz/soft on our cluster. Ask JJI about remote access.

Step 2. Setup for running 3d building

• Move the software you downloaded to a folder named ~/soft.
• Copy your openeye license to ~/.oe-license.txt
• Copy your jchem license to ~/.jchem-license.cxl

Step 3. Check out SMILES from the central server for building

• ZINC22:Checkout

4. Run 3D building (at scale)

• Building_The_3D_Pipeline_ZINC22 for information on running the script.

5. Check 3D back into UCSF Central server

• you need credentials ask chemistry4biology at gmail dot com
• ZINC22:Checkin 3D