Hi,
Unfortunately I dont think that will work because the hbond series data
sets are not created until the trajectories are actually processed (since
hbond doesn't know a priori if the hydrogen hond will actually exist). The
easiest way is probably the two-pass approach. Let me know if you have any
problems with the commands.
Good luck,
-Dan
On Tuesday, February 24, 2015, Jose Borreguero <borreguero.gmail.com> wrote:
> 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
> <javascript:;>> wrote:
>
> > Hi,
> >
> > On Tue, Feb 24, 2015 at 11:16 AM, Jose Borreguero <borreguero.gmail.com
> <javascript:;>>
> > 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
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org <javascript:;>
> > > 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 <javascript:;>
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org <javascript:;>
> 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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Received on Tue Feb 24 2015 - 11:30:04 PST
