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Input PDB file of the protein. (Waters and unrecognized small molecules will be removed)
Input SDF file containing all the conformers of the protein ligand (if available)
Generate ligand conformers with the BCL
Maximal number of ligand conformers to generate:
Use the starting coordinates in the SDF
X coordinate of ligand starting position:
Y coordinate of ligand starting position:
Z coordinate of ligand starting position:
Number of structures to generate:
The PDB chain letter to use for the ligand:
Maximum radius to search (in Angstroms) from starting coordinate:
Number of Monte Carlo sampling steps to make in low-resolution sampling:
Randomize the initial position of the ligand with a given radius (in Angstroms):
Size (in Angstroms) of the low-resolution grid. Should be greater than the length of the ligand plus the maximum search radius:
Size (in Angstroms) of the low-resolution translation Monte Carlo step:
Size (in degrees) of the low-resolution rotation Monte Carlo step:
Total cycles of highres docking to perform:
Repack every nth cycle of highres docking: