Tried performing docking using AutoDock4.
The code used is:
"autodock4.exe -p styrene_final.dpf -l styrene.dlg"
But getting the following error:
"autodock4.exe: FATAL ERROR: insufficient grid points"
Tried performing the grid step again, still getting the same error. How do I resolve this.??
You need to check your grid parameters in the dpf file. Make sure you set the correct grid size and resolution. If the grid size is too small, it won't provide enough points for an accurate docking calculation. Additionally, you can increase the search space by increasing the number of grid points. If the resolution is too low, the grid points will be too widely spaced to provide reliable results. You may also need to adjust other parameters such as the number of rotatable bonds and number of atoms to make sure they are set correctly.
Vishal Chanda When you run AutoDock4, the "insufficient grid points" error message indicates that the grid size used for docking computation may not be large enough to cover the full binding location. This can happen if the grid box is not defined properly or if the grid spacing is too coarse.
Here are some possible solutions to this problem:
1. Increase the grid box size: Check that the grid box size defined in the DPF file (styrene final.dpf) is large enough to cover the whole binding site. You may expand the grid box by modifying the grid center and grid dimensions in the DPF file.
2. Reduce grid spacing: Reducing grid spacing in the DPF file will increase the number of grid points. Lowering the grid spacing improves accuracy while increasing computing complexity.
3. Examine your coordinates: Check the coordinates in the PDBQT file (styrene.pdbqt) and that the protein and ligand are appropriately positioned in the grid box.
4. Use a pre-built grid: If your system supports it, you may use a pre-built grid for docking that has already been developed and optimized for your protein-ligand system.
5. If all of the preceding methods fail, you may need to reconstruct the grid using a new grid-generating method or program.
It's vital to remember that the grid size and spacing are linked, and changing one will influence the other. It may take some trial and error to discover the best mix for your system. It's also a good idea to study the AutoDock4 handbook for more help and troubleshooting.
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