Comments (3)
rwxayheee
commented on July 30, 2024
Hi @WesleyAC
The ligand's PDBQT file doesn't have valid 3D coordinates. With obabel, a quick fix would be:
obabel -ismiles methylphenidate.smiles -opdbqt -Omethylphenidate.pdbqt --gen3d
Let us know if that works for you
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WesleyAC
commented on July 30, 2024
Ah, that makes complete sense in retrospect! And fixes the issue. Should I close this and open a separate issue to improve the error message?
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rwxayheee
commented on July 30, 2024
Hi @WesleyAC
Yes, PR is welcome to the develop branch if you're able to provide some fixes to catch similar problems in ligand PDBQT files. Otherwise, you could leave this open or open an issue. It would be tremendously helpful if we could find out underlying problems with input files (like when angles become zero), skip the instances in batch and/or print useful help messages.
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Related Issues (20)
- Flexible docking tutorial : no HD map file after autogrid4 HOT 1
- Differences between `*_rigid.pdbqt` and `*.pdbqt` files of receptors HOT 2
- Issue : An internal error occurred in ../../../src/lib/tree.h(101) HOT 3
- Problem in generation of some map files during flexible autodock docking. HOT 3
- Error on running prepare_flexreceptor.py for flexible docking HOT 8
- Charged ligands and receptors HOT 2
- FLexible Autodock HOT 1
- Method to capture receptor structure state after flexible docking HOT 7
- Virtual screening using Python bindings HOT 22
- Autodock Vina Scoring Functions HOT 3
- How to perform docking of drugs that contain metal ions?
- REMARK VINA RESULT not in PDBQT output of `--local_only` or `--score_only` type of calculations
- Zn docking-Chelation issue HOT 9
- Discrepancy Between Multi-Ligand Docking Score and Summed Individual Scores in AutoVina HOT 6
- Multiple-ligand docking pose PDBQT cannot be (re)scored HOT 1
- What kind of file is the Linux download? HOT 2
- ERROR: Could not build wheels for vina, which is required to install pyproject.toml-based projects HOT 13
- `!pip install vina` failed in Google Colab, with a Linux Python 3 Google Compute Engine backend
- ERROR: Could not build wheels for vina, which is required to install pyproject.toml-based projects - MacOSx HOT 1
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