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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Received on Mon Oct 18 2004 - 15:53:00 PDT
