Re: [AMBER] About statistical report of 'RMS deviation from ideal bonds/angles'

From: David A Case <>
Date: Wed, 21 Jan 2015 08:06:28 -0500

On Wed, Jan 21, 2015, Yi Zhang wrote:
> I was trying to evaluate the NMR structure ensemble refined using AMBER9
> based on NOE distance and angle restraints. However, I could not find the
> statistical report of 'RMS deviation from ideal bonds/angles'. On the web
> page (, it was suggested that we could
> directly read the statistics at the end of the violation list. However, I
> can't find these reports in the output files. Does anyone know how to fix
> this?

Did you run the refinement using a parallel version of sander? The parallel
version does not report these statistics. If so, re-run a single-point
calculation (starting from the final struture), using the serial version
of the code. It will (should!) then print out the desired information.

...hope this helps...dac

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Received on Wed Jan 21 2015 - 05:30:03 PST
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