ZINC22:Building 3D

1. Download DOCK.3.8

• 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
• also at files.docking.org/private/DOCK.3.8.0.3d.tar.gz. 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 and at files.docking.org/private/software/

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

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

• need credentials