Acceptable input and output ligand file formats are:
mol2 (i.e. Tripos format)
Of the possible ligand input formats, only mol2 can be used if you wish to set ligand atom types manually.
mol (i.e. MDL sd format)
Files in mol format may also have the extension .mdl or .sdf.
mmCIF
CCD
Files utilising Chemical Component Dictionary, should have the extension .cif
Acceptable input protein file formats are:
mmCIF
mol2
pdb (.pdb or .ent)
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