Hello,
As an OpenMM developer, I'm working on improving the coverage of validation tests for our conversions of Amber force fields to OpenMM format (mostly, comparing energies of various systems with different FFs between LEaP+sander vs. OpenMM). I've traced some small differences down to ordering of the peripheral atoms in improper dihedrals. Of course this is a minor problem since the impropers will keep things planar as long as the central atom is correct, but it's annoying enough for the validation, and I'd like OpenMM to be able to reproduce the correct behavior if possible.
In particular, I've found that if the peripheral atom types for an improper in a parameter file are not in sorted order, LEaP may assign the first matching improper in the order of the parameter file, and subsequent impropers in the sorted order. Reading the thread starting at <
http://archive.ambermd.org/201305/0108.html>, this seems to be a LEaP bug related to how it saves torsion data in units when assigning parameters.
The Amber manual (section 15.1.6) says that the peripheral atom types (first, second, and fourth) are supposed to be sorted to begin with, but some Amber force field files violate this rule. For instance, in LEaP, load leaprc.protein.fb15 and save parameters for the sequence { ACE PHE PHE NME }. The first PHE will get the improper CD1-CD2-CG-CB, and the second PHE will get the improper CB-CD1-CG-CD2. The improper type is CA-CA-CA-6F at line 1975 of frcmod.fb15. The first assigned improper follows the order in the frcmod, while subsequent ones use the sorted order 6F-CA-CA-CA. This is one example of the problem; I have found several others for other force fields and residues, though I don't have an exhaustive list.
I couldn't find a consensus on the correct behavior in the above linked thread, and apparently the issue hasn't been fixed. Assuming this is a bug, what is the intended correct behavior that we should try to match? When there is a discrepancy between the parameter file and the expected sorted order, should we use the order in the parameter file, or the sorted order?
Thanks,
Evan Pretti
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Received on Mon Aug 11 2025 - 16:00:02 PDT
