Re: [AMBER] .nc trajectory format

From: Neha Gandhi <>
Date: Thu, 19 May 2016 11:19:30 +1000

My apologies for this post. I specified wrong number of atoms for saving
the trajectory (using ntwprt parameter). Hence atom number mismatch in
trajectory and initial topology and coordinate files.

Many thanks.

On 18 May 2016 at 21:44, David A Case <> wrote:

> 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.
> ...thx...dac
> _______________________________________________
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Dr. Neha S. Gandhi,
Vice Chancellor's Research Fellow,
Queensland University of Technology,
2 George Street, Brisbane, QLD 4000
Research Gate
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Received on Wed May 18 2016 - 18:30:04 PDT
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