I am working on relaxing two PDB structures to do Protein Protein docking using Rosetta 3
The PDB structure is a single chain followed by a TER record and then a collection of HETATM for the ligand. The PDB has a three letter ligand term in the amino acid field and running relax.linuxgccrelease throws an error unrecognized aa VD3. I edited the PDB file and replaced with spaces and relax didn't like that either.
What do I need to do to allow HETATM?
Do I need to move the TER record to after the last HETATM?