Conformer calculation output: can it be mol2 format?

User dd0280721c

05-10-2012 09:18:02


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.

Many thanks,


ChemAxon e08c317633

05-10-2012 09:31:34

Use the -f (or --format) command line option the specify the output format.


 cxcalc conformers -m 20 -d 0.5 -l 18000 -f mol2 input_molecule.mol2 > output_conformers.mol2

User dd0280721c

05-10-2012 12:59:38

Many thanks, that has helped!