Hi,
I've looked into the pred.pdb structure you provided, and noticed unusual ordering of nucleotides (nts). As seen in the attached images, the nts on chain A (or chain B) are not continuous, as one would expect in a normal PDB structure. This out-of-order issue causes problem: for example, A.C5 and A.C6 on chain A are far off, while A.C5 and B.U6 are close. Since A.C5 and A.C6 are clearly not connected, DSSR does not calculate Dp, as designed.
I do not know which software was used to predict the structure. However, it is desirable that the RNA structure be properly formatted. Here the nts need to be properly ordered in the PDB file.
HTH,
Xiang-Jun