Re: [AMBER] .nc trajectory format

From: David A Case <>
Date: Wed, 18 May 2016 07:44:19 -0400

On Wed, May 18, 2016, Neha Gandhi wrote:
> I was following gamd tutorial using AMBER14 and AmberTools15 (after apply
> patches). Most of the time I save trajectory files in .mdcrd format whereas
> I tried saving as .nc (according to the tutorial).
> I am now trying to do post-processing using cpptraj. I get error regarding
> atom number mismatch between prmtop and .nc trajectory. The .rst file also
> has same number of atoms as in original coordinate file and prmtop file.

Can you try a short test (just a few frames saved in the trajectory),
where the only difference between two runs is the value of ioutfm?
Does analysis still work when ioutfm=0 and fail when ioutfm=1? (Make sure the
analysis is exactly the same, except for the file name in the trajin line.)
Purpose is to try to make sure the problem is really related to ioutfm,
and that you didn't accidentally make some other change when you switched
file formats.

[Before even doing this much, double/triple check that all your file names
are correct: it's very easy to make a mistake in file names.]

If this doesn't identify the problem, please post the *exact* messages
that cpptraj is giving.


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Received on Wed May 18 2016 - 05:00:03 PDT
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