Hi there!

I am currently working on the analysis of an md simualtion of a protein-DNA complex.

I tried to find a nice tool, I can use in python to do this analysis. So far I have worked with MDtraj and pytraj. Anyhow, now I am facing different problems with the calculation in oytraj and wanted to ask if someone has experience regarding this?

My problem is that pytraj always leaves a random basepair out of the calculation (only for DNA in complex, but for both of my systems) and I just do not understand why this happens. On top of that there are a few random values which are just 0, for every major groove width calculation..

I would be very grateful if someone could help me here or tell me how one can calculate these distances in python?