AMBER Archive (2004)

Subject: AMBER: Calculating H-Bond networks using ptraj

From: Thomas Steinbrecher (steinbrt_at_scripps.edu)
Date: Mon Oct 18 2004 - 09:12:05 CDT

Dear AMBER users,

I have a protein complex trajectory and would like to extract H-bonding
information from the simulation. Up to now, I did this using carnal, but
since it is retired now, I am trying to switch to ptraj.

As far as I understand the ptraj hydrogen bonding facility, there is no
concept of 'realistic' H-bond donors or acceptors hardwired into ptraj,
I have to choose these myself instead.

I was planning to do this using a ptraj script in which I have several
lines like:

acceptor THR OG1 HG1

to account for all possible protein donors and acceptors, as well as some
lines for my ligand.

My question is: Would this be the right (and easiest) way to do this and
if yes, has someone already compiled a list for all possible protein
H-bond interactions and is willing to share it?

Kind regards,

Thomas

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