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

From: Jason Swails <>
Date: Fri, 13 Nov 2015 10:42:42 -0500

On Fri, Nov 13, 2015 at 10:28 AM, David A Case <>

> 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.

​I do recall this conversation coming up before, now... Here's another
question, though -- is there anywhere that we might be *relying* on this
"rule" to get the correct behavior? That would indeed be unfortunate, but
at the very least we should be following this rule in our own parameter
files :).

> >
> > 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.

​This is probably going to be easier to do, anyway. I'll look into it.

All the best,

Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER-Developers mailing list
Received on Fri Nov 13 2015 - 08:00:04 PST
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