The problem is that you are instantiating the chains directly using the “protein” command. This automatically assigns sequential residue numbers based on the provided sequence, starting in this case with “2”. You should instead read the sequences from the PDB — this will conserve the residue numbering in the PDB file, including all gaps and insertions. Then to add the residue, use the “insertResidue” command. I’ve provided the commands for inserting a tryptophan below (just put your structure in last.1.pdb). Also, are you using MMB 2.13? This probably won’t work with earlier revisions. Also, could you post such questions on the MMB forum on
simtk.org, or to the
rnatoolbox-help@simtk.org list? Can we put this one there? That way others will benefit.
I sent you an email some months ago about a new feature that constrains backbone dihedrals on one stretch of residues to be identical to that on another stretch. Is that still something you want to use?