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

From: Brian Radak <>
Date: Wed, 23 Sep 2020 08:57:52 -0400

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
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Received on Wed Sep 23 2020 - 06:00:05 PDT
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