I want to calculate the RMSD for the individual confrmations from the output file pdbqt into to run in into a program that only accepts PDB files. I can convert pdbqt files to PDB using openbabel but how do i split the Autodock Vina pdbqt file into indivual files?
Hello
open the output pdbqt file in discovery studio software.... this will show all the conformations and also you can calculate the RMSD in the software itself..
Regards
vina_split.exe --input outputname_out.pdbqt use this command@Isma Samuel Ssekidde
Hello there, thank you very much but intended to ask if there is a way to select multiple files pdbqt files using openbabel and convert them into individual pdb files with each conformation
Hi Isma Samuel Ssekidde,
You don't need Open Babel for this task. If you want to simultaneously display the ligand and receptor, you can use molecular graphics software like PyMOL. Simply open one of the files, like the receptor in pdbqt format, using PyMOL. Then, in the same window, go to the "File" option in the top menu and select "Open" to choose the docking output file in pdbqt format. This will allow you to display the ligand on the receptor simultaneously.
Good luck
To split vina pdbqt file -You can use this command:
"C:\Program Files (x86)\The Scripps Research Institute\Vina\vina_split.exe" --input output_outfile.pdbqt
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