Use "trajout ${i}.nc" rather than "trajout ${i}.mdcrd" in cpptraj. When I follow your instructions, cpptraj warns that the "mdcrd" file extension format is not recognized and it defaults to writing a formatted file rather than a netcdf trajectory file, which is normally used to read/write trajectories.
I don't believe imin=6 existed in AmberTools19. If you are indeed using AmberTools19, then you may need to instead set imin=5.
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Received on Mon Aug 12 2024 - 09:30:02 PDT