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

From: David A Case <>
Date: Mon, 24 Jan 2022 16:43:22 -0500

On Mon, Jan 24, 2022, Piotr Cieplak wrote:

> 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.

What you quote is for the "parm.dat" file that contains general parameters
for a given force field. It is unchanged.

What John was reporting is the existence of negative value inside a "prmtop"
file, which is specific for a given system. There is no real notion of
a "next term" in a prmtop file, and the periodicities there should be
positive, although there is no particular code in Amber the requires that.
Your quote that "only the absolute value of PN is kept" indeed implies that all
PN values in the prmtop file should be positive.

I think what John has found is one example of the twenty-year-old prmtop
file where this rule is not followed.


AMBER mailing list
Received on Mon Jan 24 2022 - 14:00:03 PST
Custom Search