Comments (2)
Vina uses its own types internally, and carbons that are bound to some heteroatoms are not considered hydrophobic. So, the system with four atoms has four hydrophobic carbons, but in the original molecule atom 18 (atom 3 in the four-atom system) is not hydrophobic because it is bonded to nitrogen.
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Ah I missed that, I thought it was all done upstream of the pdbqt file. Thank you very much for your help!
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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
- An internal error occurred in ../../../src/lib/tree.h(101) HOT 3
- 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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