Hi, The goal of my project is to screen a huge database containing thousands of ligand molecules against my protein of interest. For this, I am using the Enamine database (https://enamine.net/) as a ligand repository. As a default, the database allows us to download the ligands in one single large file in .sdf format. The important thing is that all these ligands are in 2D geometry and not in 3D. Now I was trying to convert the .sdf file into .pdbqt file with 3D geometry using Open Babel 3.1.0. For this purpose, I have been using the following workflow:
Obabel -isdf EnamineLigands.sdf -O *.sdf --split. (this is to split the large sdf file into individual sdf files) Then, obabel -isdf *.sdf -opdbqt -O *.pdbqt --gen3D (to convert sdf to pdbqt in 3D at the same time) When I execute this I constantly get the following error message in the terminal *** Open Babel Error in Do 3D coordinate generation failed ============================== *** Open Babel Warning in CorrectStereoAtoms Could not correct 2 stereocenter(s) in this molecule (Spironolactone) with Atom Ids as follows: 12 19 Warning: Stereochemistry is wrong, using the distance geometry method instead Now, when distance geometry method is used by the software it gets stuck for hours and even days. Currently I am only working on a small dataset of ~ 1000 ligands and things are stuck for the last 2 days. I need help from the experts and developers. I hope I can get a work around this problem. Many thanks for reading my mail. Best regards
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