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

From: David A Case <>
Date: Tue, 22 Sep 2020 21:07:01 -0400

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 Tue Sep 22 2020 - 18:30:03 PDT
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