Re: [AMBER] trajout format with cpptraj in Ambertools 17

From: Daniel Roe <>
Date: Tue, 17 Oct 2017 11:52:07 -0400

On Tue, Oct 17, 2017 at 11:40 AM, Li, Wen <> wrote:
> and output file extension is either ncdf or something else, output
> trajectory is always formatted as NetCDF --- not Amber Coordinates format.

For sander/pmemd, trajectory output format is controlled by the ioutfm
namelist variable. Since Amber 16 the default has been NetCDF

> All these inputs worked with cpptraj in Ambertools 14 in the past while both
> input and output files were formatted as crd. Now I am wondering if trajout
> has to be associated with a specific file extension with cpptraj in
> Ambertools 17. If so, what is it? Otherwise, what would be the problem.

It's not clear to me what problem you are having. Cpptraj will
automatically detect the format of input trajectories regardless of
the extension. Output trajectory format is either selected by either a
keyword or file name extension with that priority; if neither is
present/recognized the default is Amber ASCII (although this should
probably be changed to be consistent with sander/pmemd). A list of
recognized keywords/extensions for trajectories is located in the
table in section '28.8 Trajectory File Commands' on page 580 of the
Amber 17 manual (also available via 'help trajin' or 'help trajout' in

Hope this helps,


Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
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Received on Tue Oct 17 2017 - 09:00:02 PDT
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