Hi,
Does your copy of cpptraj pass all of the test cases? Specifically
'test.framerange' (from $AMBERHOME/AmberTools/test/cpptraj type make
test.framerange). This tests the 'onlyframes' functionality, both
writing Amber trajectory and restarts. It works for me with my copy of
AmberTools 12.
-Dan
On Tue, Jul 31, 2012 at 7:46 AM, Marc van der Kamp
<marcvanderkamp.gmail.com> wrote:
> PS A related issue is that when onlyframes is specified, it appears that
> the [<fileformat>] flag is ignored, i.e. AmberTools1.5 cpptraj writes the
> default formatted AMBER trajectory file regardless, not e.g. a dcd file.
> I don't know if writing different formatted trajectory files with
> onlyframes is supposed to be supported or not, but if it isn't, it's not
> clear from the manual.
>
> On 31 July 2012 14:24, Marc van der Kamp <marcvanderkamp.gmail.com> wrote:
>
>> Hi all,
>>
>> I was trying out the 'onlyframes' option of trajout in cpptraj for the
>> first time today.
>> With cpptraj from AmberTools12, I could not get a trajectory to write,
>> with no error message listed in the output. I applied all patches available
>> this morning, recompiled but the issue remained.
>>
>> Going back to AmberTools1.5 cpptraj, I could get a trajectory to write,
>> with the exact same input. (So I've got a workaround: just use
>> AmberTools1.5 cpptraj.)
>> This is the trajout line I tested with:
>> trajout test.mdcrd onlyframes 1,5,6-8
>>
>> This was the relevant information in the output of AmberTools12 cpptraj:
>>
>> > [trajout test.mdcrd onlyframes 1,5,6-8]
>> Saving frames 1 5 6 7 8>
>> ...
>> OUTPUT TRAJECTORIES:
>> [test.mdcrd] is an AMBER trajectory, Parm 0: Writing frames 1 5 6 7 8
>>
>>
>> And this the equivalent information in the output of AmberTools1.5 cpptraj
>>
>> > > > [trajout test.mdcrd onlyframes 1,5,6-8]
>> Saving frames 1 5 6 7 8
>> ...
>> OUTPUT TRAJECTORIES:
>> [test.mdcrd] is an AMBER trajectory, Parm 0 (with box info)
>>
>>
>> Is this a bug in AmberTools12 cpptraj?
>>
>> Thanks,
>> Marc
>>
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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
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Received on Tue Jul 31 2012 - 07:00:03 PDT
