I have an SDF of docking results generated in smina (spin-off of AutoDock VINA with the ability to handle SDFs). Each compound has five poses that were generated, but I need to get rid of all but the best-scoring one for each compound. E.g. for compound #1654, five poses are returned with energies of -8.0, -7.9, -7.8, -7.7, and -.7.6. I just want to keep the one that scored -8.0. Is there a way to do this in Maestro, Discovery Studio, MOE, or OpenBabel? Or does anyone have a shell script to do this?
To get the best ranked poses of each ligand, you can use sdsorter as described in smina tutorial available at https://sourceforge.net/projects/smina/files/?source=navbar
The tutorial file is called "custom_scoring.pdf" which is attached to this comment. Commands for sdsorter are available in this tutorial. Also, you can select only the X top ranked compounds to the output file using the "-nbest X" flag.
Hi Vitor, thanks for your answer--sdsorter worked perfectly. The "-nbest" flag took the top X compounds overall, not the top X poses from each docked compound, but the "-reduceconfs" flag did exactly what I wanted. Thanks!!
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