Re: [AMBER] How does tleap detect improper torsions?

From: Matias Machado <>
Date: Wed, 23 Sep 2020 11:24:06 -0300 (UYT)

Just a follow up to David's...

This information is now very well documented in the new AMBER 20 Reference Manual []

You can find it at Chapter "14. Reading and modifying Amber parameter files", within the section "Torsion Terms" (pag. 252)... search for "Out-of-Plane Terms".

The only missing concept is about wild cards, which are read at their actual position (e.g. x-dd-cc-bb is load as x-bb-cc-dd).

Despite recognising that re-ordering doesn't affect the improper definition as long as the central atom is the same, it does generate a so called "improper term nightmare" in case of coarse-grained models (e.g. SIRAH), which doesn't follow a symmetric phase in 180º as all-atoms models do.

Anyway... in the future I would love to see leap reading the given definition instead of doing some re-ordening... that would be much easy to understand, develop and transfer...



Researcher at Biomolecular Simulations Lab.
Institut Pasteur de Montevideo | Uruguay

----- Mensaje original -----
De: "Brian Radak" <>
Para: "AMBER Mailing List" <>
Enviados: Miércoles, 23 de Septiembre 2020 9:57:52
Asunto: Re: [AMBER] How does tleap detect improper torsions?

That helps immensely - thank you.

The alphabetical rule is likely what is goofing us up and this can be
implemented and tested easily enough.


On Tue, Sep 22, 2020, 9:07 PM David A Case <> wrote:

> On Tue, Sep 22, 2020, Brian Radak wrote:
> >
> >
> >** Warning: No sp2 improper torsion term for aa-bb-cc-dd
> >
> >Where I've used dummy types for illustrative purposes. What's confusing
> >is that the loaded frcmod clearly has an improper defined for
> >aa-cc-bb-dd -- why does tleap ignore this? When I swapped the atom order
> >manually, the warning goes away and I've confirmed that one extra
> >improper appears in the prmtop.
> For tleap, aa-bb-cc-dd is not the same as aa-cc-bb-dd, since in the
> first case cc is the third (central) atom, and in the second case it is
> bb. I'm pretty sure (and it seems to match your experience) that tleap
> does not try to see if any reordering of atoms might make sense -- it's
> pretty strict in what it considers a "match".
> For regular torsions, tleap knows that aa-bb-cc-dd is the same as
> dd-cc-bb-aa. For impropers, this is the rule as I understand it:
> the third atom (cc in aa-bb-cc-dd) is the central one, and the other
> three atoms (aa,bb,dd) must be in alphabetical order by atom type.
> ...does this help? ....thx...dave
> _______________________________________________
> AMBER mailing list
AMBER mailing list

AMBER mailing list
Received on Wed Sep 23 2020 - 07:30:02 PDT
Custom Search