AMBER: Calculating H-Bond networks using ptraj

From: Thomas Steinbrecher <>
Date: Mon, 18 Oct 2004 07:12:05 -0700

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,


The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Mon Oct 18 2004 - 15:53:00 PDT
Custom Search