No input file or format spec or possibly a misplaced option. Most options must come after the input files. (-i -o -O -m can be anywhwere.) Open Babel 2.3.2 -- Jul 26 2017 -- 20:11:55 Usage: obabel [-i<input-type>] <infilename> [-o<output-type>] -O<outfilename> [Options] Try -H option for more information.

Open Babel converts chemical structures from one file format to another Usage: obabel[-i<input-type>] <infilename> [-o<output-type>] -O<outfilename> [Options] The extension of a file decides the format, unless it is overridden by -i or -o options, e.g. -icml, or -o smi See below for available format-types, which are the same as the file extensions and are case independent. If no input or output file is given stdin or stdout are used instead. More than one input file can be specified and their names can contain wildcard chars (* and ?). The format of each file can be different unless the -i option has been used, when they are all the same. By default, the molecules are aggregated in the output file, but see -m option, Splitting, below. Options, other than -i -o -O -m, must come after the input files. Conversion options -f <#> Start import at molecule # specified -l <#> End import at molecule # specified -e Continue with next object after error, if possible -z Compress the output with gzip -k Attempt to translate keywords -H Outputs this help text -Hxxx (xxx is file format ID e.g. -Hcml) gives format info -Hall Outputs details of all formats -V Outputs version number -L <category> Lists plugin classes of this category, e.g. <formats> Use just -L for a list of plugin categories. Use -L <ID> e.g. -L sdf for details of a format or other plugin. -m Produces multiple output files, to allow: Splitting: e.g. obabel infile.mol -O new.smi -m puts each molecule into new1.smi new2.smi etc Batch conversion: e.g. obabel *.mol -osmi -m converts each input file to a .smi file For conversions of molecules Additional options : -d Delete hydrogens (make implicit) -h Add hydrogens (make explicit) -p <pH> Add hydrogens appropriate for this pH -b Convert dative bonds e.g.[N+]([O-])=O to N(=O)=O -r Remove all but the largest contiguous fragment -c Center Coordinates -C Combine mols in first file with others by name --filter <filterstring> Filter: convert only when tests are true: --add <list> Add properties from descriptors --delete <list> Delete properties in list --append <list> Append properties or descriptors in list to title: -s"smarts" Convert only if match SMARTS or mols in file: -v"smarts" Convert only if NO match to SMARTS or mols in file(not displayed in GUI) --join Join all input molecules into a single output molecule --separate Output disconnected fragments separately --property <attrib> <value> add or replace a property (SDF) --title <title> Add or replace molecule title --addtotitle <text> Append text to title --writeconformers Output multiple conformers separately --addoutindex Append output index to title --0xout <file.xxx> Additional file output --addfilename Append input filename to title --AddInIndex Append input index to title --AddPolarH Adds hydrogen to polar atoms only --align Align coordinates to the first molecule --canonical Canonicalize the atom order --fillUC <param> Fill the unit cell (strict or keepconnect) --gen2D Generate 2D coordinates --gen3D Generate 3D coordinates --genalias Generate aliases as an alternative representation. --highlight <param> Highlight substructures in 2D depictions --largest # <descr> Output # mols with largest values --partialcharge <method> Calculate partial charges by specified method --readconformer Adjacent conformers combined into a single molecule --sort <desc> Sort by descriptor(~desc for reverse) --unique [param] remove duplicates by descriptor;default inchi Interface to OBAPI internals API options, e.g. ---errorlevel 2 errorlevel # min warning level displayed To see a list of recognized file formats use babel -L formats [read] [write] To see details and specific options for a particular format, e.g CML, use babel -L cml