missing basepair when calculating major groove width

[cloudella48]

Hi there!
I have also posted in the issues section, because I am really lost right now.
I have a 70 bp long DNA in complex with a protein. I have done an all atom simulation in GROMACS and want to analyse the results now. For this purpose I want to use pytraj. When I calculate the major groove distances, I noticed that:

1. there are always a few random values which are equal to 0
2. one base pair is missing in each of my two simulations. It is one random basepair in the middle of my DNA and I do not understand where this error is coming from.

I would be very grateful, if someone could help me here!