Reply To: trying to create heme.params

[Anonymous]

For what it’s worth, I’ve never had any issues with .mol2 files, at least on the OpenBabel/Avogadro produced structures I’ve used.

The particular issue you’re running into is the nc bond type to the iron is not currently recognized by molfile_to_params (although it is a valid bond type by the mol2 standard). I can update the code in the development version, but for your purposes I’ll suggest either using the .mol format as Steven suggests, or, if you want to use the user supplied charges in the .mol2 file, hand edit the .mol2 file to change the nc bond types to single bonds (“1”). I admit that might not be ideal, but it should result in a ligand topology file which works adequately.

Rocco Moretti