Hi,
Thank you very much for improving cpptraj.
I've just tested the new version and the program (working on a corrupted
trajectory file) now stops silently, without any error but also without
any message that something goes wrong. I attach the output from our
testcase.
I compared the size of the output files and saw that most of the files
are now larger than before.
> file size-before size-after diff
> _MMPBSA_complex.mdcrd.0 49938530304 50738174577 +
> _MMPBSA_complex.pdb 745472 751799 +
> _MMPBSA_dummycomplex.inpcrd 338807 338807
> _MMPBSA_dummyligand.inpcrd 1292 1292
> _MMPBSA_dummyreceptor.inpcrd 337603 337603
> _MMPBSA_ligand.mdcrd.0 177602560 180449279 +
> _MMPBSA_ligand.pdb 0 2708 +
> _MMPBSA_receptor.mdcrd.0 49761148928 50557950378 +
> _MMPBSA_receptor.pdb 745472 749098 +
> output-cpptraj.txt 8790016 10955 -
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
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 Mon Dec 19 2022 - 13:00:02 PST
