Dear Daniel,
I was able to bypass writing the hbond series to a file since I already
know the bond I seek (ASP_196.OD1-WAT_370.O-H2)
The commands are:
hbond H1 donormask :370.O donorhmask :370.H2 acceptormask :196.OD1
filter H1[solutehb] min 0.5 max 1.5
#some magic here
Thanks a lot!
-Jose
On Tue, Feb 24, 2015 at 1:51 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> On Tue, Feb 24, 2015 at 11:16 AM, Jose Borreguero <borreguero.gmail.com>
> wrote:
> > I want to retain only (or at least operate on) those frames for which a
> > particular hydrogen bond is present. Can I use the output of the hbond
> > command to set up a condition to filter out frames lacking the bond, or
> at
> > apply some other command only to the frames fullfiling the hydrogen bond
> of
> > interest?
>
> Yes, via the 'filter' action in cpptraj. For example, say that you
> have saved your hydrogen bond time series data in a file called
> solutehb.dat, and the hydrogen bond of interest is in the third
> column:
>
> #Frame NDP_269.O14-ILE_192.N-H ALA_92.O-NDP_269.N3-H64
> 1 1 1
> ...
>
> You could do something like (using the same trajectories used to
> generate the hydrogen bond data):
>
> parm myparm.parm7
> trajin mytraj.nc
> readdata solutehb.dat name H1
> filter H1:3 min 0.5 max 1.5
> <more actions>
>
> Now only frames for which the data in H1:3 (third column of the data
> previously read in) are between 0.5 and 1.5 will be allowed through to
> subsequent actions, which works since hbond series data is 1 for
> hydrogen bond present and 0 otherwise.
>
> Note that hbond 'series' data is not written out by default, so you
> have to explicitly write the data like so:
>
> parm myparm.parm7
> trajin mytraj.nc
> hbond H1 nointramol avgout hbavg.dat series
> run
> writedata solutehb.dat H1[solutehb]
>
> Hope this helps,
>
> -Dan
>
> >
> > Best,
> > Jose Borreguero
> > _______________________________________________
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> > 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)
>
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>
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Received on Tue Feb 24 2015 - 11:30:03 PST
