Hi again,
My problem was with writing a .dcd format using AmberTools1.5 cpptraj and
onlyframes; the following input is giving me a AMBER coordinates trajectory
instead:
trajout test1out.dcd dcd onlyframes 1,3-4
However, AmberTools12 does write a dcd file as requested (now it works for
me with onlyframes again...).
So, all is good!
Thanks,
Marc
PS The output from AmberTools1.5 cpptraj in the above test does indicate a
dcd file will be written:
> [trajout test1out.dcd dcd onlyframes 1,3-4 ]
TrajectoryFile debug level set to 5
CpptrajFile: [test1out.dcd] FMT CHARMMDCD, TYPE UNKNOWN_TYPE, ACC W
SetBaseFilename: Filename is test1out.dcd
Base filename is test1out.dcd
Ext= .dcd Len= 4
DEBUG: Setting up WRITE for file test1out.dcd
[test1out.dcd] is format CHARMMDCD and type STANDARD with access W
TrajectoryIO debug level set to 5
Saving frames 1 3 4>
...
OUTPUT TRAJECTORIES:
[test1out.dcd] is a CHARMM DCD file Little Endian 32 bit, Parm 0: Writing
frames 1 3 4, 93332 atoms, Box 0, seekable 0
On 31 July 2012 17:16, Jason Swails <jason.swails.gmail.com> wrote:
> On Tue, Jul 31, 2012 at 11:52 AM, Daniel Roe <daniel.r.roe.gmail.com>
> wrote:
>
> > 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.
> >
>
> To pitch in here with Dan, MMPBSA.py uses the onlyframes argument to
> outtraj/trajout in order to write NetCDF files, and I've never seen
> problems. I would look carefully at the cpptraj output, as it will tell
> you if there were any ignored arguments.
>
> The trickiest may be DCD files, especially if you are used to how ptraj
> used to deal with them (note, for dcd files you need to apply the bug fixes
> to fix how cpptraj deals with box information in explicitly solvated
> systems). In ptraj, you used the keyword "charmm" to denote a dcd
> trajectory output. In cpptraj, however, you need to use the keyword "dcd".
>
> Future versions of cpptraj will have file type recognition based on file
> name suffix (so *.dcd will automatically be DCD, etc.) -- thanks Dan!
>
> Jason
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Tue Jul 31 2012 - 09:30:04 PDT
