Required Parameters

-in <filename>

File containing a molecule to be fit to density.

File type

Extension

SMILES

.smi .ism .smi.gz .ism.gz

OEBinary

.oeb .oeb.gz

SDF

.sdf .mol .sdf.gz .mol.gz

MOL2

.mol2 .mol2.gz

PDB

.pdb .ent .pdb.gz .ent.gz

MacroModel

.mmod .mmod.gz

-out <filename>

File containing resulting conformations exported in the following formats:

File type

Extension

OEBinary

.oeb .oeb.gz

SDF

.sdf .mol .sdf.gz .mol.gz

MOL2

.mol2 .mol2.gz

PDB

.pdb .ent .pdb.gz .ent.gz

MacroModel

.mmod .mmod.gz

-map <filename>

Input density grid used to fit ligand. Note that mtz files have additional settings, see MTZ File Options

Grid File type

Extension

MTZ

.mtz

OpenEye

.grd

Grasp

.phi

CCP4

.map .ccp4

XPLOR

.xplor xplmap

ASCII Grid

.agd