The first problem is that the TNT geometry library requires that the first two bases in DNA be connected via the d5'END link instead of the normal dSUGPHOS link. If this correction in not made TNT will complain about the absence of some atoms which are not supposed to be present. The progress of refinement will not be affected.
The second problem is that TNT cannot distinguish between DNA and RNA. The bases in DNA are connected using the dSUGPHOS link in the sequence file while RNA bases should be connected using the SUGPHOS link. If your model contains RNA you will have to edit the sequence file.