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
>
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Received on Tue Jul 31 2012 - 07:00:02 PDT
