I've submitted this request a few times over the past month, never really looking too far into what might be causing the error. Today, however, I checked my pdb files and they have the same numbering and chain identification yet the error is the same. This is a pdb of an RNA under two conditions (one is the crystal structure, one is our model of an intermediate). Can you suggest any way forward?
The most common problems arise from use of a flavor of the PDB format that the morph server doesn't recognize, as you may be doing for the modelled structure. You could try submitting a truncated version of the the crystal structure (which I'm guessing you downloaded from the pdb) as structure 1, change a few coordinates, and submit that modified file as structure 2. This will give us a quick test to determine if it is your modelled structure that is causing the problem.