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

From: Niel Henriksen <shireham.gmail.com>
Date: Fri, 13 Nov 2015 09:42:37 -0800

Hi All,

Thanks for your analysis. I am actually less worried at the moment about
whether the specific torsion SHOULD overwrite the generic torsion or not.
 (Although it would be nice to have this cleared up.) What worries me is
that the behavior is not consistent within the same molecule for identical
chemical groups. Some of the "hc-c3-c -o" connectivities show that the
generic torsion IS getting removed, whereas in other "hc-c3-c -o"
connectivities it is NOT removed ... all within the same molecule.

Perhaps there is some subtle reason why this behavior is correct. But if
it is a bug, then it doesn't matter what we decide is the correct behavior
because it appears that LEaP is already not following the "rules"
consistently.

--Niel
ps, I attached .mol2, .frcmod, and tleap.in file for anyone who wants to
debug

On Fri, Nov 13, 2015 at 7:42 AM, Jason Swails <jason.swails.gmail.com>
wrote:

> On Fri, Nov 13, 2015 at 10:28 AM, David A Case <david.case.rutgers.edu>
> wrote:
>
> > 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
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
> _______________________________________________
> AMBER-Developers mailing list
> AMBER-Developers.ambermd.org
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>


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Received on Fri Nov 13 2015 - 10:00:04 PST
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