Re: [AMBER] NetCDF trajectory file does not contain information about time/timestep

From: Daniel Roe <>
Date: Fri, 17 May 2019 10:25:00 -0400


On Wed, May 15, 2019 at 2:13 PM Karolina Mitusińska (Markowska)
<> wrote:
> Now when I use Amber18/AmberTools18 to preprocess files (for example to
> skip some frames) I'm getting errors that my trajectory file does not
> contain informations about the time/timestep.

So cpptraj didn't really handle time info in NetCDF files well in past
versions - in some cases I think the time information was silently
removed :-(. More recent versions of cpptraj (including I believe AT
18) behave properly, i.e. they keep all information in the input
trajectory unless directed otherwise. The more recent versions of
cpptraj will also let you know if the time information is missing. You
can also quickly check if your NetCDF trajectory contains time info by
doing 'ncdump -h <file>' and checking for the existence of the
'time(frame)' variable.

Hope this clears things up (and apologies to all for old cpptraj's bad


> Did something change? And most important: how to make cpptraj to include
> such information into the trajectory file?
> Looking forward to help from you.
> Best regards
> Karolina Mitusińska
> PhD student
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Received on Fri May 17 2019 - 07:30:03 PDT
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