Re: [AMBER] nativecontacts command in CPPTRAJ

From: Daniel Roe <>
Date: Tue, 22 May 2018 09:33:38 -0400


On Tue, May 22, 2018 at 9:25 AM, Ruth Helena Tichauer <> wrote:
> Dear Amber developers,
> I’ve been trying to use the nativecontacts command without success so I’m posting again the question I’d asked few days ago.

Andreas suggested that you may need the non-native option
('savenonnative' etc) of the native contacts command, but you don't
appear to have tried it. Please read the Amber manual entry for the
'nativecontacts' command for more details.

> Prior, I used the cat linux command to append several trajectories into a single one, but instead of getting a trajectory containing around 5000 frames I get one with 250 frames only, which corresponds to a single portion of my simulation.. This is the exact command in case you could help me spot a mistake:

Yikes - don't do this! In most cases the 'cat' command should not be
used to string together formatted files, and certainly not binary ones
like the NetCDF format. The correct way to concatenate trajectories is
to read them into a trajectory processing program (like cpptraj) and
output them, e.g.


Hope this helps,


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Received on Tue May 22 2018 - 07:00:02 PDT
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