Yes, this answers my question.
Thank you very much for your time and help!
Best regards,
Andrzej
On 20.12.2022 19:44, Daniel Roe via AMBER wrote:
> 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 Wed Dec 21 2022 - 00:30:03 PST
