[Open Babel] pdb -> mol2 conversion with halides

[Jon W. <jo...@ga...>]

Hi

I'm trying to convert from pdb to mol2 and in the main its working well
but there is a minor irritation. If a CL or BR is included in the pdb file
in the mol2 file it become C. or B

Also is there any way to have more than one molecule in the PDB file and
to convert the lot to mol2 with one command. The orginal babel managed
this but I can not seem to get openbabel to recognise more than one
molecule per file.

Can anyone suggest fixes please?

Thanks
Jon