Re: [AMBER] Troubleshooting script <measure_equil_rmsd.ptraj>

From: Daniel Roe <>
Date: Thu, 6 Jan 2011 09:47:28 -0500


The issue appears to be here:

On Wed, Jan 5, 2011 at 11:12 AM, George Tzotzos <> wrote:
> PTRAJ: reference 2ogn_3og_solv.inpcrd
> PTRAJ: rms reference out equil.rmsd .CA,C,N
> WARNING in ptraj(), rms to reference: missing reference structure.
> Set this prior to this rms with the command "reference"
> Ignoring command...

This indicates that for some reason the reference structure you
specified (2ogn_3og_solv.inpcrd) did not load correctly. Check that
this reference structure matches the prmtop you are using. Also, try
to load 2ogn_3og_solv.inpcrd in a separate ptraj run:

trajin 2ogn_3og_solv.inpcrd

And see if any error messages pop up. Let me know if you have any more issues.


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Received on Thu Jan 06 2011 - 07:00:02 PST
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