I think my first question is whether 3upo_protein.pdb exists in the directory. If so, can Open Babel read it on the command line?
obabel 3upo_protein.pdb -O 3upo.mol2 # this will attempt to convert the PDB file to Mol2 -Geoff >> --receptor 3upo_protein.pdb\ >> --residue B:SER222\ >> --outputfile ligcovalent.pdb > ============================== > *** Open Babel Error in ReadFile > Cannot read from 3upo_protein.pdb > [ ERROR ] Fail to read molecule "3upo_protein.pdb" ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
