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
>
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Received on Tue Jul 31 2012 - 07:30:02 PDT
