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
Received on Tue Jul 31 2012 - 09:30:03 PDT
