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

From: John Chodera <john.chodera.choderalab.org>
Date: Sun, 23 Jan 2022 18:58:51 -0800

Amber devs,

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 [
https://ambermd.org/Amber20_Benchmark_Suite.tar.gz], which contains
negative entries for DIHEDRAL_PERIODICITY in its prmtop file.

I am aware that frcmod files can use negative periodicities (PN), but this
does not appear to be sensible for prmtop files, and the repeated negative
periodicities in the prmtop do not appear to have originated from a
negative iPN in a prmtop because the repeated terms share the same

Is this a bug in the FactorIX benchmark prmtop? Or is this a valid (but
undocumented) feature of prmtop DIHEDRAL_PERIODICITY values?

We are tracking this issue here on the OpenMM issue tracker:

Apologies for spamming the mailing list, but I couldn't locate the proper
channel for raising an issue on the development repository.



John D. Chodera
Associate Member, Computational and Systems Biology Program
Memorial Sloan-Kettering Cancer Center
BIH Einstein Visiting Fellow, Charité Universitätsmedizin, Berlin
email: john.chodera.choderalab.org
office: 646.888.3400
fax: 646.888.3105
mobile: 415.867.7384
url: http://www.choderalab.org
AMBER mailing list
Received on Sun Jan 23 2022 - 19:00:02 PST
Custom Search