Just a follow up to David's...
This information is now very well documented in the new AMBER 20 Reference Manual [
http://ambermd.org/doc12/Amber20.pdf]
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...
Best,
Matías
------------------------------------
PhD.
Researcher at Biomolecular Simulations Lab.
Institut Pasteur de Montevideo | Uruguay
[
http://pasteur.uy/en/labs/biomolecular-simulations-laboratory]
[
http://www.sirahff.com]
----- Mensaje original -----
De: "Brian Radak" <brian.radak.gmail.com>
Para: "AMBER Mailing List" <amber.ambermd.org>
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.
Cheers,
Brian
On Tue, Sep 22, 2020, 9:07 PM David A Case <david.case.rutgers.edu> 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
>
>
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Received on Wed Sep 23 2020 - 07:30:02 PDT
