Our users often write us asking about building blocks. In ZINC15 there are some improved ways to do this.
I am trying to download the csh mol2 script for Unix but the file is not being found. Could you please fix the file? Or is there another way to download the zbb database?
First, you might just want to browse them and see what you're going to get.
Once you are ready to download, begin with 1000 SMILES:
wget -o log -O bb.smi "http://zinc15.docking.org/substances/subsets/bb.smi?count=1000"
Is that what you wanted? Perhaps you wanted only purchasable building blocks?
Is that right? Perhaps you only wanted ones that are in stock for 2-week delivery. In this case, use
Did you want some extra information for each one, like molecular weight and logP?
Now, perhaps you wanted 2D SDF format, for use in DataWarrior or InstantJchem?
Finally, you are ready to download them all. Change 1000 to all. It will take a while, since there are millions of qualifying molecules.
Perhaps you were really only interested in a particular functional group. For instance, primary amines:
That is, 1000 building blocks that are for sale and containing a primary amine, in 2D SDF format containing data tags for ZINC ID, molecular weight and logP.
Oh, wait, when you look at them, you realize that you want only molecules containing a primary amine, but without a carboxylate. So do this.
There may be some duplicates in these later queries. We're aware of that and we're working to fix it.
We hope you find this useful.