On Tuesday, February 24, 2015, Jose Borreguero <borreguero.gmail.com> wrote:
> 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.
My two favorite words when it comes to cpptraj. Let me know if you have any
more questions.
-Dan
>
>
> On Tue, Feb 24, 2015 at 2:20 PM, Daniel Roe <daniel.r.roe.gmail.com
> <javascript:;>> 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
> <javascript:;>>
> > 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:;>
> > > <javascript:;>> wrote:
> > >
> > > > Hi,
> > > >
> > > > On Tue, Feb 24, 2015 at 11:16 AM, Jose Borreguero <
> > borreguero.gmail.com <javascript:;>
> > > <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
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> > > >
> > > >
> > > >
> > > >
> > > > --
> > > > -------------------------
> > > > 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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> > >
> >
> >
> > --
> > -------------------------
> > 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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> http://lists.ambermd.org/mailman/listinfo/amber
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--
-------------------------
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 - 14:00:02 PST
