Comments (1)
diogomart
commented on July 28, 2024
Hello,
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the scripts are here: https://github.com/ccsb-scripps/AutoDock-Vina/tree/develop/example/autodock_scripts
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search dimensions and precalculated grid maps (i.e. the box) are always required. The best is to use a molecular visualizer (pymol, vmd, autodocktools/pmv, chimera, AGFR-gui) to see how the box fits the receptor. Ligands will dock inside that box because there is an energy penalty for ligand atoms that go outside during the search. Deciding the box location and dimensions is subjective and depends on where you want ligands to dock.
from autodock-vina.
Related Issues (20)
- Details on scoring function terms HOT 3
- Autogrid4 Atom Type Error with Large Ligand Database HOT 6
- An internal error occurred in ../../../src/lib/parse_pdbqt.cpp(69). HOT 3
- Autogrid4 raise error "dyld: Library not loaded:" HOT 8
- Enormous free energy of binding HOT 6
- Weird protein split in flexible docking HOT 7
- Is AutoDock-Vina applicable to peptides? HOT 3
- Docking to zinc atoms in a non-3,1 tetrahedral conformation HOT 4
- Vina flexible docking HOT 4
- PyPi suggests windwos compatibility of python bindings.
- rdkit.six not found HOT 1
- Problems with Binary installation HOT 1
- Autogrid4 Unknown receptor type: HOT 1
- Vina runtime error: The ligand is outside the grid box HOT 1
- I am getting this error while doing flexible autodock docking HOT 1
- H-bond term HOT 2
- 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
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from autodock-vina.