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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.126.96.36.199d.tar.gz
- also at files.docking.org/private/software/DOCK.188.8.131.52d.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
3. Check out SMILES from the central server for building
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