I am trying to parameterize an NCAA which is a result of cyclization of the backbone, rather than just a PTM of an R group. I am using the molfile_to_params_polymer.py script (BTW is there a python 3 version of this script?)
The connection points are at the R group of one residue, though there is a break in the chain (C=O -> C-OH) then a connection point to the nitrogen backbone atom of the subsequent residue.
When I use fixbb to modify to this residue I am getting the error:
ERROR: In ICOOR atom line in topology file: ./GYS.params; reference atoms must be specified in earlier line. Missing N or LOWER or O
I've attached the molfile and params files below. Please let me know if there is a way to add some lines to the params to indicate this connection.
Thanks in advance!