AMBER Archive (2009)

Subject: [AMBER] Variations of the number of total hydrogen bond in MD simulations using ptraj

From: workalemahu berhanu (
Date: Sun Aug 16 2009 - 15:13:21 CDT

Dear amber users
I would like to analysis my trajectory file for the change in the
total number of hydrogen bonds in my peptide and peptide with ligand
which is having beta sheet secondary structure in MD simulation. Is it
possible to do it using ptraj? Could anyone provide me a script for
this kind of analysis?
Thank you
With regards

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