I’ve sucesfully finished a test run with my protein and managed to screen 20K ligands and my first impressions of VirtualFlow are good; relatively easy to use with prior experience in docking. Nice work!
Now the problem, during the post processing I was able to extract the poeses winning structures as a compoundID.pdbqt file. However, how/where can I find the name of this compound and where to buy it? Since all ligands are originated from the enamine REAL database, Ive tried searching the ID on their website, unfrotunalty I was not able to find the compound. I have also tried drawing the structure and searching it like that on several databases, but no luck!
Any methods on how to get the ligand name efficiently?
head -n 100 ../../ranking/qvina02_rigid_receptor1/firstposes.all.minindex.sorted.clean > compounds
creates a list called compounds containing the top 100 docking poses with their respective score.
However, after running
vfvs_pp_prepare_dockingposes.sh ../../../output-files/complete/qvina02_rigid_receptor1/results/ meta_collection compounds dockingsposes overwrite
I only get one file with the docking poses of only my winning structure. How to alter the command that it produces a file with the docking poses of the top 100 ligands?