AMBER impropers are only good for planar purposes for exactly this reason.
On 9/24/20 8:56 AM, Brian Radak wrote:
> 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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Received on Thu Sep 24 2020 - 10:30:02 PDT
