Sorry, I forgot the sandwich the 'go' command:
hbond H1 donormask :370.O donorhmask :370.H2 acceptormask :196.OD1
go
filter H1[solutehb] min 0.5 max 1.5
This works.
On Tue, Feb 24, 2015 at 2:20 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> 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)
> > >
> > > _______________________________________________
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> > > 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)
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Tue Feb 24 2015 - 12:00:29 PST
