Re: [AMBER] Negative DIHEDRAL_PERIODICITY in prmtop for amber20-benchmark FactorIX benchmark

From: Piotr Cieplak <>
Date: Mon, 24 Jan 2022 20:39:44 +0000 (UTC)

 As stated in JACS1995v117p5179 "The periodicity of the torsion. A negative
value is not used in the calculation but signifies more than one component
around a given bond." The negative value of pn is used only for identifying
the existence of the next term and only the absolute value of PN is kept.
Has this changed in the new topology format?

    On Monday, January 24, 2022, 06:47:55 AM PST, David A Case <> wrote:
 On Sun, Jan 23, 2022, John Chodera wrote:

>Recently, OpenMM added some sanity checking code to help ensure
>non-physical parameters were not specified. This flagged an issue with the
>FactorIX benchmark system from the Amber20 benchmark suite [
>], which contains
>negative entries for DIHEDRAL_PERIODICITY in its prmtop file.

The factor_ix benchmark prmtop file is indeed ancient: it was originally
an "old-style" topology, which means that it was created before 2000,
certainly using force fields that are no longer relevant.

SO: please let us know if you sanity checks find other examples of negative
dihedral periodicities.  I have a (very vague) recollection of seeing this
problem before, and fixing the underlying force field files.

About the factor_IX benchmark: the first simple task (volunteers, please!)
would be to manually change the five negative entries to be positive, and see
if the results change.  If we are lucky, we can just update the prmtop file.

Thanks for the report.....dac

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