Hi Dan,
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.
I'm not sure what has changed in between - perhaps it had to do with the
location I was reading the trajectories from (a mounted remote file system)
and AT12 cpptraj was unlucky enough to run into issues whereas AT1.5
cpptraj was not??
Apologies for 'wasting' your time!
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.
--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
>
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Received on Tue Jul 31 2012 - 09:00:02 PDT
