[Chimera-users] Doubts about DOCK6.9 and ZINC20

Francesca Magarotto - francesca.magarotto2@studio.unibo.it francesca.magarotto2 at studio.unibo.it
Tue Jul 20 00:14:28 PDT 2021

I’m a student and I’m currently doing a thesis.
I’ve never used Dock or Chimera before, so I followed some tutorials but now I’m a bit confused.
1. For five months I’ve saved the prepared receptors and the ligands as mol2, but I didn’t choose “write current selection to @SETS section of file”.
I’ve just read on Chimera that it “makes the currently selected atoms as a SET (as used to specify the rigid portion of a ligand in DOCK)”. The docking I’ve performed seemed to go, but is actually everything wrong because I didn't select the option?
2. I’ve generated the receptor without hydrogens after dockprep (so after assigning charges and hydrogens). I’ve deleted only hydrogens but maybe the charges are still there, is that an error?
3. I’ve always saved the receptor without hydrogens in mol2 instead of pdb, because I’ve seen this in some tutorials, but now I’ve read tutorials that save it in pdb.
Is this another error?
I was able to generate the surface even with mol2 no hydrogens receptor and I’ve always toggle on “use untrasformed coordinates”, but obviously the options to save the file change for mol2 and pdb.
4. I follow a tutorial online to download 3D molecules from ZINC20. Anodyne means there are no PAINS and no reactive groups? Is the most “clean” reactivity pattern?
5. I don’t know how to organize all the directories and subdirectories downloaded with ZINC. I downloaded them in format mol2 and method curl, is that correct or shoul I use fot the virtual screening another format and method?
To perform a virtual screening, I need to save them in a single mol2 file? How can I do that without errors? I've seen the option "flat" in downloading method in ZINC, is this a way to download the molecules correctly for virtual screening?
6. I need to use Chimera, but even with ViewDock I’m not able to open so many molecules (190 822), how can I look at the results in the end?
7. I’ve saved the ligands’ mol2 files using sybyl-style hydrogen naming. Is that an error?
8. To perform the virtual screening using 3D molecules from the tranche browser of ZINC20, can I use them as they are or I need to edit them in some way (for example after downloading them, open them in Chimera and using add H and/or add charge)?
I need very specific indications about all these questions, because I’ve never done something similar, it’s the very first time with all and I’m afraid of making mistakes.
I apologize for the many questions, but I hope that someone can answer all my doubts.
Thank you,
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