Thank you everyone for your help. Greatly appreciated!
On Wed, May 23, 2018 at 1:33 AM Gustaf Olsson <gustaf.olsson.lnu.se> wrote:
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> 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
> run
> 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 <jlb1692.msstate.edu> 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
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Received on Wed May 23 2018 - 07:00:02 PDT
