Your problem is with the 3'-terminal residue. You have asked that no patch should be applied to the 3'-terminal ("last none"), and this is probably not what you want. It leaves you wtih a 3'-terminal residue trying to link to a non-existent following residue. The warnings regarding the 5'-terminal residue can safely be ignored since the refer to atoms that have been actively deleted by the 5ter patch, in contrast to atom "+P" which is expected at the non-patched 3'-terminal. You can remove the WARN keyword to avoid having all these warnings listed.
Last edited by lennart; 04/17/20 01:52 PM.