Hey, I got the results in PDBQT format. The file contains atomic indexes preserved from the underlying SDF file.
Now I would like to compare the RMSD between the results from AutoDock Smina with other programs., But first I need to convert my PDBQT to SDF format. However, I don't know how to do it to keep the appropriate indexes in the file.
Could anyone help me?
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You should be able to use obrms (from openbabel) and not have to worry about file format conversion (and the RMSD will be symmetry corrected if need be).
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Thank you! I have one more question, because I know that openbabel has a Python package, is it possible to do it in Python, and if so, do you know how?
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afaik isn't pybel an openbabel wrapper for Python, I might be wrong. And also I think there is a UI tool for openbabel for mac https://macinchem.org/ibabel/
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
Hey, I got the results in PDBQT format. The file contains atomic indexes preserved from the underlying SDF file.
Now I would like to compare the RMSD between the results from AutoDock Smina with other programs., But first I need to convert my PDBQT to SDF format. However, I don't know how to do it to keep the appropriate indexes in the file.
Could anyone help me?
I am attaching the files.
2vnt_output.pdbqt - output of smina
2vnt_ligand.sdf - reference
2vnt_ligand.pdbqt - converted reference to docking
You should be able to use obrms (from openbabel) and not have to worry about file format conversion (and the RMSD will be symmetry corrected if need be).
Thank you! I have one more question, because I know that openbabel has a Python package, is it possible to do it in Python, and if so, do you know how?
No, it is a commandline tool. But rdkit GetBestRMS will also do what you want.
afaik isn't pybel an openbabel wrapper for Python, I might be wrong. And also I think there is a UI tool for openbabel for mac https://macinchem.org/ibabel/
Thanks so much. I found that openbabel has integrated python package with rmsd tools.