Re: [AMBER] Warning when trying to get RMS

From: Daniel Roe <>
Date: Thu, 14 May 2015 13:14:49 -0600

On Thu, May 14, 2015 at 12:56 PM, Mohammad Salem
<> wrote:
> I get this error message from CPPTRAJ upon trying to get the RMSD from a protein trajectory:
> "Warning: Coordinates are being rotated and box coordinates are present.
> Warning: Unit cell vectors are NOT rotated; imaging will not be possible
> Warning: after the RMS-fit is performed.”

Does the calculation not actually complete or is this the only
warning? This warning message (not an error) is to let you know that
once your system has been rotated it is no longer in alignment with
the original unit cell, hence any subsequent imaging operation will be
incorrect. As long as you don't plan on doing any imaging (or
calculating imaged distances etc) after the RMS-fit everything should
be fine. This warning has been put in explicitly because people would
occasionally try to image after rms-fitting and then wonder why they
ended up with weird artifacts in the resulting systems.

Hope this helps,


> Any insight?
> Regards,
> Mohammad
> _______________________________________________
> AMBER mailing list

Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Thu May 14 2015 - 12:30:03 PDT
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