AMBER Archive (2009)

Subject: Re: [AMBER] missing violations of the covalent geometry

From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Tue Apr 07 2009 - 06:10:42 CDT

On Tue, Apr 07, 2009, Helena P M Tossavainen wrote:
>
> After a successful simulated annealing run I obtain the list of NMR
> restraint violations, made by the LISTOUT=POUT command. However, the lines
> "RMS deviation from ideal bonds/angles" are missing.

Are you running a parallel simulation? The RMS deviations mentioned
above are only printed for a serial simulation (since we never actually
communicate the needed information to all nodes in parallel.) I
generally run a final, one step, serial minimization at the end to get
these statistics.

...dac

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