ZINC22:Building 3D: Difference between revisions
Jump to navigation
Jump to search
(asdf) |
(Redirected page to Building The 3D Pipeline ZINC22) Tag: New redirect |
||
| (6 intermediate revisions by one other user not shown) | |||
| Line 1: | Line 1: | ||
#REDIRECT [[Building The 3D Pipeline ZINC22]] | |||
This describes how to become a contributor to ZINC-22 | |||
= 1. Download DOCK.3.8 = | = 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. | * 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 | * 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 | * 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 python3 environment (lig_build_py3-3.7.1.tar.gz) | ||
| Line 13: | Line 15: | ||
* Clone submission scripts to somewhere you can use them. (https://github.com/btingle/zinc-3d-build-3.git) | * 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 | * 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 = | |||
= 2. Setup for running 3d building = | |||
* Move the software you downloaded to a folder named ~/soft. | * Move the software you downloaded to a folder named ~/soft. | ||
| Line 22: | Line 23: | ||
* Copy your jchem license to ~/.jchem-license.cxl | * Copy your jchem license to ~/.jchem-license.cxl | ||
= 3. Check out SMILES from the central server for building = | = Step 3. Check out SMILES from the central server for building = | ||
* [[ZINC22:Checkout]] | |||
= 4. Run 3D building (at scale) = | = 4. Run 3D building (at scale) = | ||
| Line 30: | Line 33: | ||
= 5. Check 3D back into UCSF Central server = | = 5. Check 3D back into UCSF Central server = | ||
* need credentials | * you need credentials ask chemistry4biology at gmail dot com | ||
* [[ZINC22:Checkin 3D]] | |||
= 6. Lather, rinse, repeat, go back to step 3 = | |||
[[Category:ZINC22]] | [[Category:ZINC22]] | ||
Latest revision as of 18:07, 9 March 2023
Redirect to:
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)
- 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