Thanks very much Daniel! That sounds like just what I wanted. I will try
what you suggested over the next couple of days.
Thanks again.
On Tue, Sep 23, 2014 at 3:01 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> This can be done using the 'outtraj' command with the 'maxmin'
> keyword. It can be done in 2 stages. In the first stage you generate
> hydrogen bond data vs time using the 'hbond' command with the 'series'
> keyword, e.g.:
>
> hbond H1 series .N,H,C,O
>
> This will create a data set for each solute-solute hbond detected,
> named H1[solutehb]:X, where X is a unique internal index for that
> hydrogen bond. The name of each of these data sets is listed after the
> run completes, e.g.:
>
> DATASETS:
> 20 data sets:
> H1[UU] "H1[UU]" (integer), size is 100
> H1[solutehb]:24 "GLU_13.O-VAL_2.N-H" (integer), size is 100
> H1[solutehb]:104 "TYR_11.O-ILE_4.N-H" (integer), size is 100
> ...
>
> These time series data sets contain a '1' when the hydrogen bond in
> question is present and '0' when not. After running (because the data
> sets are not actually created until hydrogen bonds are detected) you
> can write these out to a separate data set for further processing or
> use them in the same run (or both). Once you have the data it can be
> used with 'outtraj' with the 'min' and 'max' keywords set so that data
> with '1' indicates frames should be written. So the entire command
> sequence might look like:
>
> hbond H1 series .N,H,C,O
> run
> # Save time series data for later just in case
> writedata solutehb.dat H1[solutehb]
> # Write out frames where "GLU_13.O-VAL_2.N-H" is formed
> outtraj E13O-V2H.nc netcdf maxmin H1[solutehb]:24 min 0.5 max 1.5
>
> A related command is 'filter', which lets you process only frames that
> match certain criteria with subsequent actions.
>
> Hope this helps,
>
> -Dan
>
> On Tue, Sep 23, 2014 at 5:57 AM, George Green <soyo.green.gmail.com>
> wrote:
> > I have been doing some hydrogen bond analysis and have obtained
> occupancies
> > and other data for solute-solute hydrogen bonds using AMBER 13.
> >
> > I would like to output some frames from the trajectory based on this
> > analysis, so that I can look at structures that have certain specific
> > hydrogen bonds. e.g. If there is a hbond between res37 and res44, I would
> > like to output all frames that possess this interaction.
> >
> > Is there any way to do this with cpptraj?
> >
> > many thanks for your assistance.
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 307
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-6208 (Fax)
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Tue Sep 23 2014 - 07:30:03 PDT
