Required Parameters

Input Files Option

Either option -in or option -complex must be used to perform a SZYBKI run.

-in <filename>

Molecular input file name containing 3D coordinates in any format supported by OEChem. In order to comply with the previous SZYBKI releases, an alias -i can be used instead of -in. This option might be used as a keyless parameter without the -in or -i keys but only when used last or next to last when the last option on the command line is -out. Warning: File name: szybki_out.oeb is used as the default output file name, so should be avoided as an input file name.

-i <filename>

An alias to -in.

-ligands <filename>

An alias to -in.

-protein <filename>

Protein input file with 3D coordinates in any format supported by OEChem. Works in combination with the -in option. No removal of pre-existing ligands in file filename will be done as in the case of the -complex option. This option can be aliased with -p for compatibility with previous SZYBKI releases.

-p <filename>

An alias to -protein.

-complex <filename>

Input file with 3D coordinates of a protein-ligand(s) complex in any format listed in the table above. All ligands contained in the molecule file filename will be optimized one by one in the presence of all others.

Input file formats

SZYBKI can handle molecular files in the following formats:

SZYBKI file format support
File extension Description
mol MDL Mol File
mmd, mmod Macromodel
mol2 Tripos Sybyl mol2 file
oeb New Style OEBinary
pdb Protein Databank PDB file
sd, sdf MDL SD File
xyz XMol XYZ format