ZINC22:Building 3D

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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

4. Run 3D building (at scale)

5. Check 3D back into UCSF Central server

6. Lather, rinse, repeat, go back to step 3