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MD simulations / Filter frayed ends or broken H bonds

« on: October 10, 2019, 08:32:20 am »

Hello,

I am trying to process some X-ray protein-DNA crystal data. I am just focussing on the double-stranded DNA structure. But there are some snapshots/structure in which the H-bond doesn't seem to be okay i.e. say distance of acceptor and donor atoms in H-bond is more than 5 angstrom.

Are there any justified criteria for how to filter such bad snapshots?

Thanks in advance
Rahul