Reply To: some application troubles when using resfile flag

[Anonymous]

When a PDB is read in, this warning is placed for every heavy atom missing in the input. If you place a copy of your adduct in the input PDB, with all the atoms in place and named as in the params file, then the warnings will go away. They are only warnings: so long as the PDB-reading machinery knows what residue it is, it will fill in the missing atoms for you from the params file.