I downloaded the AA tranche from ZINC as a pdbqt.gz file. Following decompression of the file, can I go straight to docking using Raccoon or do I need to upload to ADT and add charges, all hydrogens, and merge non polars?
If I need to go through ADT first, a subfolder of one tranche contains a single pdbqt file for 15 ligands. Interestingly, when I open the file on pymol it shows only 1 ligand and not all 15 of them. Why is this happening? How can I go about saving all the ligands from ADT into one pdbqt file because right now ADT is only letting me save one of the ligands shown on pymol, even if I hide everything.
Hi Elina Kadriu ,
Use openbabel to convert your ligand molecule to .pdbqt
You can download the library of large no of compounds. ex . zinc database (https://zinc.docking.org/).
You can use autodock vina to screen the molecule library (http://vina.scripps.edu/manual.html#screening )
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