Hi,
On Mon, Dec 19, 2022 at 3:52 PM Andrzej Dorobisz via AMBER
<amber.ambermd.org> wrote:
>
> So how to interpret this? Did cpptraj abort silently its work due to an
> error, or does it just skip bad frames and finishes it work normally. It
So what's happening here is cpptraj is soldiering on through the bad
frames, which is why the output trajectories are larger. I'm guessing
the MMPBSA input doesn't have a 'check' in there, so the bad frames
are not skipped. That's why I recommended running the trajectory
through cpptraj with 'check skipbadframes' to generate a trajectory
without the corruption, then use that trajectory through mmpbsa. At
this point it would be up to the mmpbsa devs to add a check phase if
it were to be incorporated into mmpbsa itself. Personally I think it's
a good idea to check your trajectory before you run any further
analysis on it (even a simple 'rmsd' to first frame calc should have
revealed the corruption through weird looking rmsd spikes).
Hope this answers your questions,
-Dan
> would be useful to see some kind of message in the output file.
>
> Regards,
> Andrzej
>
>
> On 16.12.2022 19:00, Daniel Roe via AMBER wrote:
> > Hi,
> >
> > I've made a couple of updates to cpptraj that will improve handling of
> > corrupted trajectories
> > (https://github.com/Amber-MD/cpptraj/pull/1009). The upshot is you can
> > use the 'check' action with the 'skipbadframes' option to filter out
> > the corrupted frames:
> >
> > parm myparm.top
> > trajin corrupted.nc
> > check skipbadframes reportfile report.dat
> > trajout ok.nc
> >
> > The OMP version should provide some speedup for the 'check' action.
> > Hope this helps,
> >
> > -Dan
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Received on Tue Dec 20 2022 - 11:00:03 PST
