Hi,
On Tue, Jul 31, 2012 at 9:38 AM, Marc van der Kamp
<marcvanderkamp.gmail.com> wrote:
> Whilst trying to make a small test-case (with just a few frames), I have
> not been able to reproduce the error.
> To my surprise, the original job works as well now.
Computers can be annoying like that :-). However, if you can ever
reproduce the problem and you have the time please send a test case my
way.
> Apologies for 'wasting' your time!
Not a waste - bug reports from the community are what keeps software healthy.
> What remains, is that it wasn't clear from the manual that only the default
> trajectory output (formatted AMBER crd) can be written when using
> onlyframes. Not a big deal of course, as it can be converted to other
> formats once it is created.
Any format can be written with the 'onlyframes' option; it's a keyword
that can be specified in addition to any of the other 'trajout'
options (this is in fact the reason why the test case writes both a
trajectory and restarts with 'onlyframes'). If you find that trajout
with 'onlyframes' is ignoring a specified format please let me know,
that would be a bug.
-Dan
>
> --Marc
>
> On 31 July 2012 15:18, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
>> Since the test cases pass I need more info to know what is going wrong
>> where. Can you attach the complete cpptraj output (add the commands
>> 'trajindebug 5' and 'trajoutdebug 5' to the beginning of your input so
>> that more info is printed), and if possible send me off-list your
>> topology and a frame (or a couple) of your trajectory so I can try and
>> reproduce the issue? Thanks.
>>
>> -Dan
>>
>> On Tue, Jul 31, 2012 at 8:08 AM, Marc van der Kamp
>> <marcvanderkamp.gmail.com> wrote:
>> > Hi Dan,
>> >
>> > The test.framerange test passes:
>> >
>> > $ make test.framerange
>> > **************************************************************
>> > TEST:
>> >
>> /gpfs/cluster/chem/chmwvdk/amber12/AmberTools/test/cpptraj/Test_trajout_framerange
>> >
>> > CPPTRAJ: Trajout Frame Range [Amber Restart]
>> > diffing test.rst7.3.save with test.rst7.3
>> > PASSED
>> > ==============================================================
>> > diffing test.rst7.5.save with test.rst7.5
>> > PASSED
>> > ==============================================================
>> > diffing test.rst7.6.save with test.rst7.6
>> > PASSED
>> > ==============================================================
>> > diffing test.rst7.7.save with test.rst7.7
>> > PASSED
>> > ==============================================================
>> > diffing test.rst7.8.save with test.rst7.8
>> > PASSED
>> > ==============================================================
>> >
>> > CPPTRAJ: Trajout Frame Range [Amber Coordinates]
>> > diffing framerange.crd.save with framerange.crd
>> > PASSED
>> > ==============================================================
>> >
>> > I haven't done a full test yet after applying all bug fixes earlier, but
>> > before applying AT 12 patches 8 to 16, all cpptraj tests passed as well.
>> >
>> > Thanks,
>> > Marc
>> >
>> > On 31 July 2012 14:49, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>> >
>> >> 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
>> >> >>
>> >> > _______________________________________________
>> >> > AMBER mailing list
>> >> > AMBER.ambermd.org
>> >> > http://lists.ambermd.org/mailman/listinfo/amber
>> >>
>> >>
>> >>
>> >> --
>> >> -------------------------
>> >> 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) 585-9119 (Fax)
>> >>
>> >> _______________________________________________
>> >> AMBER mailing list
>> >> AMBER.ambermd.org
>> >> http://lists.ambermd.org/mailman/listinfo/amber
>> >>
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>>
>> --
>> -------------------------
>> 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) 585-9119 (Fax)
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
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) 585-9119 (Fax)
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Jul 31 2012 - 09:00:03 PDT
