Re: [AMBER-Developers] Leap inconsistencies with wildcard torsion (surprise)

From: David A Case <>
Date: Fri, 13 Nov 2015 10:28:57 -0500

On Fri, Nov 13, 2015, Jason Swails wrote:
> What's happening here is that the
> generic torsion defines periodicity 2, while the specific torsion assigns
> periodicity 1 and 3. So there is no term for the specific torsions that
> overwrites the periodicity-2 term that is assigned by the generic torsion.

This is a repeat of a discussion we've had several times in the past. The
current rule is supposed to be that any specific torions should explicitly
override all the periodicities of the generic torsions. But I agree that it
may be all-too-easy for this "rule" to get violated.

> 2. After all torsions have been assigned, go through and delete the ones
> that are tagged as wild-card for 4 atoms that *also* have specific torsions
> assigned
> 3. Same thing as 2, except just set the force constant to the wild-card
> torsions to 0 so they don't add to the potential.

Both of these should not be done silently, but with appropriate messages to
the user. If there are generic periodicities that are not being over-ridden by
specific ones, that is likely to be an error. So, from this point of view,
solution #3 sounds fine...the zero terms themselves flag potential problems,
and there should be only a few of those.


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Received on Fri Nov 13 2015 - 07:30:08 PST
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