[AMBER] Water bridge analysis using cpptraj (hbond)

From: Abhilash J <md.scfbio.gmail.com>
Date: Fri, 18 Jan 2019 19:34:06 +0530

Hi everyone,

  I have a trajectory of ligand-protein complex.
  From visualizing some parts of the trajectory i know that there is a
ligand-water-water-residue interaction in some frames.
  I want to select those frames in which this interaction takes place using
hbond command (getting total number of frames in which this occurs is also
required) .
  I was able to calculate ligand-water-residue (water bridge) interactions
but unable to get ligand-water-water-residue ones.
  Is it possible to get this information with hbond.
  I read some old AMBER archives in which Dan has mentioned few things in
this regard but i could not figure out completely, how to go about it in my
  Any help will be appreciated.


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Received on Fri Jan 18 2019 - 06:30:04 PST
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