Re: [AMBER] Autoimage command not working

From: Daniel Roe <>
Date: Tue, 15 Jan 2019 14:46:23 -0500


On Tue, Jan 15, 2019 at 2:35 PM Martín Pettinati
<> wrote:
> Hi,
> The error messages were stated in the original email. It appears to be some problem with the topology file.

Sorry, I meant what was the error you experienced using 'fixatomorder'.

> Cpptraj version is 17 and the the input is

In general, it's best to use the latest version.

> Adding "fixatomorder" before "autoimage" makes it so autoimage is indeed performed but "fixatomorder" modifies the topology file and I can't save it because "parmout" and "outparm" commands (stated in the users manual) aren't working. I would need this modified topology file to visualize the output file propperly.

The re-ordered topology can be written via the 'outprefix' keyword,
and the re-ordered trajectory can be written via a 'trajout' command,

parm myparm.parm7
fixatomorder outprefix reordered

Hope this helps,


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Received on Tue Jan 15 2019 - 12:00:04 PST
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