Thanks for the notes Matias.
We do not use wildcards - - instead our atom types are assigned uniquely
since we only have one or two ligands at a time.
Do I understand correctly that tleap will in fact (silently) change the
explicit improper definitions based on the alphabetical rule? For purely
planar terms I don't know off hand if this actually matters (probably not
for energies, maybe for forces?)
On Wed, Sep 23, 2020, 10:24 AM Matias Machado <mmachado.pasteur.edu.uy>
wrote:
> 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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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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Received on Thu Sep 24 2020 - 09:00:03 PDT
