Selecting tranches in ZINC22
Current method to select tranches to dock in ZINC 22 .
We support three platforms:
- our cluster, .txt suffix
- Wynton, .wyn suffix
- AWS, .s3 suffix
If you are on another platform, suggest using one of these three.
We have created subsets for you (see below, but you can select subsets at a very fine grain level:
- by HAC by number of atoms
- by calculated LogP within 0.1 units.
- by charge -4 to +4.
Look in /nfs/exd/zinc-22/sets/
- if you want to dock lead-like, you want
/sets/H17-19.lead-like.<suffix> where <suffix> is txt, wyn or s3 as above /sets/H20-23.lead-like.<suffix>
Then, depending on whether you want to include H24 and H25, you can optionally include
If you want to add on compounds from calculated LogP from 4.0 to 4.9
/sets/H17-19.greasy-leads.<suffix> and so on as above
- if you want to dock fragments H10-H16, LogP<4
- if you want to dock calculated logP > 5
- if you want to dock big monsters (not recommended, but who knows)
You can learn about how the sets were assembled using make-sets.csh make-sets.csh in turn uses files in /nfs/exd/jjiwork/dirs/ these in turn are created using make-files2.csh in /nfs/exd/jjiwork/
We can adjust these subsets based on what people want. It is easy, we just need to do it.
real life example
So, supposing I want to dock lead-like (H17-H25) in AWS using my S3 bucket results2021. I assemble a file database210325.txt from four files:
cat H17-19.lead-like.s3 H20-23.lead-like.s3 H24.lead-like.s3 H25.lead-like.s3 > database210325.txt
I upload this to s3
aws s3 cp database210325.txt s3://results2021/
Then I go on AWS and I follow the instructions in DOCK on AWS.
I monitor the job as it runs.
Then I harvest the results and download them to my computer.