Hi,
You can do this in cpptraj with the 'filter' command, which filters
frames for subsequent actions based on given data sets and ranges. For
example, say you only want to look at frames that fall within 0-90
degrees for a certain dihedral:
dihedral d1 <dihedral args>
filter d1 min 0 max 90 out FilteredFrames.dat
<more actions>
In this case, only frames that are between 0 and 90 for dihedral d1
will continue to be processed, otherwise all subsequent
actions/trajectory output will be skipped. FilteredFrames.dat will
contain a 1 for frames that were processed and 0 for frames that were
filtered. Note that you can filter on multiple data sets (e.g. an
angle and a distance etc). See the manual for more details.
Hope this helps,
-Dan
On Tue, May 6, 2014 at 2:34 PM, Eugene Yedvabny <eyedvabny.berkeley.edu> wrote:
> Hello Amber community,
>
> Is it possible in cpptraj to do processing on only a subset of mdcrd
> frames, with that subset determined by the output of a previous command?
> For example, I would like to load an mdcrd, calculate the phi or chi
> dihedral and then perform secstruct and hbond analysis on a subset of
> frames that fall within a certain dihedral range. Another option would be
> to just create a new 'sub-trajectory' with frames that fit the dihedral
> range, but per Amber manual I can only specify the start/end frames to
> trajout, not an array of frame numbers.
>
> Presently I am doing such post-processing by printing out the entire series
> data and then running the statistics in python, but that is proving to be
> cumbersome and lacks the full information that gets printed out in the
> summary files for the whole trajectory.
>
> Thank you,
> Eugene Yedvabny
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
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 May 06 2014 - 14:00:03 PDT
