I am trying to convert a large single file library (.sdf, .pdb) containing 50k+ molecules into a .pdbqt file for screening. I have tried using AutoDock Tools but it crashes upon trying to load the library. I have also tried Open Babel, but it only converts the first couple molecules. The one successful attempt I had at converting them left out the "MODEL" and "ENDMDL" text at the end of each file, which is required for use in Vina. Could anyone give me some recommendations how you go about doing such conversions? Thanks!
Try to separate components inside sdf file with openbabel:
openbabel -i bigfile.sdf -O bigfile2.sdf --separate
then split input files into separate components:
openbabel -i bigfile2.sdf -O smallfiles/file.pdbqt -m
If this doesn't do the trick, please investigate, why it works only until a certain molecule (" it only converts the first couple molecules") - maybe something is wrong with a single molecule and it makes the program crashes?
Adrian Bebenek you can use pyrx just for converting sdf files to pdbqt files then pick them up from the working directory for pyrx but you will not be able to convert easily more than 1000 ligands per one you should split them.
or you can use some scripts via python on Linux it will convert them easily.
best regards
I think the best option is to make a script to prepare your pdbqt files. You can use the python scripts available in autodock tools to add hydrogens, charges (if needed and not calculated previously) etc.
Here is the official guide to help you with that: http://autodock.scripps.edu/faqs-help/tutorial/using-autodock4-for-virtual-screening
Filip Stefaniak Vitor Rabelo thank you for the recommendations!
Anas Alobaidi, do you happen to know how I could convert these files on Pyrx and access them from the working directory? Ive been able to upload my library, but in the "save as" functionality I do not see a .pdbqt option.
In case you tend to use Autodock for the same, there is a python script found in Utilities24 folder: prepare_ligand.py
try it!
Hi Adrian Bebenek
Open-Bable can make your task easier,(http://openbabel.org/wiki/Main_Page)
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