On Mon, Mar 3, 2014 at 6:08 PM, Ahmed Ayoub <atayoub.ualberta.ca> wrote:
> Dear Amber Developers,
>
> I have been trying to submit an MMPBSA parallel job. The job works
> perfectly fine on AmberTools 12 perfectly fine. But on AmberTools 13 it
> keeps giving me this error although the trajectory files are fine:
>
Does it work in serial?
> TrajError: start frame (1) > total frames (0)
>
> Error occured on rank 0.
>
> Exiting. All files have been retained.
>
There are a number of things that might be going wrong here. First,
strip_mask may be set incorrectly (do you have any water molecules or ions
that you included as part of your receptor?) Second, you might be asking
for more processors than you have snapshots in your trajectory. Since
MMPBSA.py.MPI parallelizes by splitting up frames, you could wind up with
these kinds of errors.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue Mar 04 2014 - 14:00:03 PST
