I am trying to dock some small peptides. I'm getting good results but the final peptide ligand file format is causing some problems. Is there any way to get Dockingserver to save/retain all of the standard amino acid residue data in the final docked PDB file? If not, can you suggest an easy way to convert to a PDB file format that treats the peptide ligand as a protein? Thanks.

Thank you for your question, we are testing this issue and will inform you soon, how this problem can be solved.

The requested feature has been added to DockingServer, thus, DS is now able to treat peptide ligands. Subscribers can download the docked ligand (with sequence information reserved) by clicking on the geometry tab on the download link.