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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--
-------------------------
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 - 11:00:07 PST
