Re: [AMBER] Hydrogen Bond Occupancy

From: Gustaf Olsson <>
Date: Wed, 23 May 2018 06:27:45 +0000

Assuming all you files are in one directory, this is a layout for a ptraj input file I use when evaluating hydrogen bonds between specific pairs of atoms.

# your PRMTOP filename
parm [PRMTOP-FILE].prmtop
# I output 1ns blocks so modify this part to only include the trajectory files
# corresponding to the time-period you wish to analyse
trajin [TRAJECTORY-FILE-50ns].mdcrd
trajin [TRAJECTORY-FILE-51ns].mdcrd
trajin [TRAJECTORY-FILE-52ns].mdcrd
trajin [TRAJECTORY-FILE-53ns].mdcrd
trajin [TRAJECTORY-FILE-54ns].mdcrd
trajin [TRAJECTORY-FILE-55ns].mdcrd

trajin [TRAJECTORY-FILE-100ns].mdcrd
# The rest is the evaluation details
hbond S1 series out [SERIES_OUTPUT_FILENAME].out \
# run “hbond” and output series data to [SERIES_OUTPUT_FILENAME]
# this is included for the final life-time calculation, if not desired you could
# exclude this
donormask :XXX.XXX donorhmask :XXX.YYY \
# If you want to analyse specific donors and acceptors, specify the :residue.atom
# on which the hydrogen atom involved is attached (X) followed by the specific
# :residue.hydrogen (Y) on that same residue (X)
acceptormask :ZZZ.ZZZ \
# then specify the bond accepting :residue.atom
avgout [AVERAGE_OUTPUT_FILENAME].out nointramol
# This outputs the "occupancy" results
runanalysis lifetime S1[solutehb] out [LIFETIME_OUTPUT_FILENAME].out
# This runs the hydrogen bond analysis follows by the lifetime evaluation, exclude
# the runanalysis part if lifetimes are not investigated.

You run this analysis with:

cpptraj -i [INPUT_FILENAME].ptraj

This will analyse the occupancy and lifetimes of interactions for the hydrogen atom YYY attached to atom XXX on the residue XXX and the accepting atom ZZZ on residue ZZZ

Regarding how to specify donors and acceptors, consult the manual. You can for instance just specify a wider “donormask/accetormask” as :XXX and have ptraj look for suitable atoms, however this outputs all the found interactions in one file. I am a lazy person and my simulations usually requires detailed output for a lot of interaction-pairs so I usually output each sought after interaction to a separate output file so I don’t have to sort though the data manually.

Hope this helps you a bit and good luck!

// Gustaf

> On 22 May 2018, at 19:13, Jerrano Bowleg <> wrote:
> Dear Amber Users,
> I would like to perform a hydrogen bond analysis to identify the hydrogen
> bond occupancies for each guanine tetrad in G-quadruplex DNA. I have
> already performed MD simulation of 100 ns and I would to get the
> occupancies of each tetrad over the last 50 ns of simulation.
> Any ideas on how to acquire this information?
> Thanks
> Jerrano L. Bowleg
> Graduate Student
> Dr. Steven Gwaltney Lab
> Mississippi State University
> _______________________________________________
> AMBER mailing list

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Received on Tue May 22 2018 - 23:30:02 PDT
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