I had some issues today using some PDBs generated by Modeller, and I tracked the error to the fact the TER fields inside the PDB have more columns (which should not be there)
For example
ATOM 1393 C2' DT D 35 81.341 17.516 55.945 1.00 48.63 C
ATOM 1394 C3' DT D 35 82.152 18.800 55.754 1.00 48.81 C
ATOM 1395 O3' DT D 35 83.036 19.108 56.819 1.00 49.40 O
TER 1396 DT D 35
ATOM 1397 N SER A 20 33.719 48.929 107.140 1.00 49.89 N
ATOM 1398 CA SER A 20 34.080 48.490 108.522 1.00 50.05 C
ATOM 1399 CB SER A 20 33.010 48.924 109.527 1.00 50.13 C
I understand that the TER separator is not supposed to have anything afterwards. Is there a particular reason why Modeller is writing my TER records like that? It should read only "TER"
Best
Pedro