Hm, I think what's happening here is trajout is going by the absolute frame
number instead of relative to the output trajectory itself but I need to
run some tests. I'll get back to you - thanks for the report.
-Dan
On Tuesday, February 24, 2015, Jose Borreguero <borreguero.gmail.com> wrote:
> Dear amber users,
>
> I don't know whether this is the intended use for trajout or a bug. I have
> the following script:
>
> parm junk.top
> trajin junk.dcd
> readdata junk.dat name H2
> filter H2:2 min 0.5 max 1.5
> trajout junk.pdb pdb start 1 stop 1 offset 1
>
> I want to save as "junk.pdb" the first frame for which H2:2 lies in between
> 0.5 and 1.5. On the other hand, what is saved is just the first frame of
> junk.dcd. Thus the filtering condition is ignored when passing options
> "start 1 stop 1 offset 1" to trajout.
>
> For my intended use, I have to piece the script into two scripts:
>
> parm junk.top
> trajin junk.dcd
> readdata junk.dat name H2
> filter H2:2 min 0.5 max 1.5
> trajout intermediate.dcd dcd #only H2:2 min 0.5 max 1.5 frames are saved
>
> parm junk.top
> trajin intermediate.dcd
> trajout junk.pdb pdb start 1 stop 1 offset 1
>
> Best,
> Jose
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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 - 17:30:02 PST
