I am using the conformer generator on the command line, using the following argument:
cxcalc conformers -m 20 -d 0.5 -l 18000 input_molecule.mol2 > output_conformers.mol2
My input file contains a single molecule in mol2 format.
The calculation runs fine (i.e. I get conformers), but the resulting output file is actually in SD format, rather than the mol2 format I wanted.
Is there a specific option I need to add to ask Marvin to output in mol2 format? Or is it simply not possible? I wish to avoid going to SD format and converting back to mol2 format as some bond types are changed when I do that conversion.