[Chimera-users] Saving ligand and protein as a single PDB

Hello, I am planning to run a docking simulation in a different program, and I need to have a "reference ligand" included in the PDB file. The particular PDB I am working on does not have a ligand included. So I am trying to position one using Chimera. I started with the protein file and a ligand file (ligand is in .mol2 format). I loaded both into Chimera, and I correctly positioned the ligand relative to the PDB. I then saved both using File -> Save PDB... I choose to save the file relative to the protein, and I select "save multiple models: in a single file". However, when I load the file into the docking program, it does not show the ligand. Additionally, there are a few structural errors in the output PDB file. Please advise. Thanks, Nancy