On Fri, Nov 13, 2015 at 12:16 PM, Jason Swails <jason.swails.gmail.com>
wrote:
> A minor nit here -- I don't think terms ever get *removed* -- it's just
> that the generic terms are not always added first, it would appear. Only
> if the generic terms are added first, and the specific ones added later,
> would the periodicity 2 values crop up.
>
> As this is, if not explicitly documented, *known* behavior, we really have
> to fix gaff.dat to specifically override generic torsions
>
>
>
oh, ok. I was just going by what the comment said in the tleap code you
linked:
"if the previous torsion is general and this one is specific, delete the
previous one(s) and add the new one"
It's odd that the generic terms are not always added first. Must have to
do with atom ordering.
> >
> >
> >
> > 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.
> >
>
> Actually, according to tleap there are no rules here -- we are firmly in
> the realm of undefined behavior. The rule is imposed on the construction
> of the parameter files -- not on tleap. If a torsion type has a matching
> generic term, then any specific term that matches a subset of the generic
> term's applicability has to override every periodicity term that generic
> term defines *in addition to* whatever other terms it wants to add.
>
This is where I meant that tleap is not following the rules. I assumed
that adding generics first was a rule, but now I know better :)
> So the problem is really that gaff.dat does not contain a 3rd line for
> c3-c3- c- o that defines a term with periodicity 2 and force constant 0.
> In that case, every instance in the prmtop will have the same 3 terms.
>
>
Yeah, that is the solution we noticed in parm10.dat:
HC-CT-C -O 1 0.80 0.0 -1. Junmei et al,
1999
HC-CT-C -O 1 0.00 0.0 -2. Explicit of
wild card X-C-CT-X
HC-CT-C -O 1 0.08 180.0 3. Junmei et al,
1999
> I will see if I can work up a quick script to highlight offending specific
> terms in the gaff database and get this file fixed.
>
>
Thanks!
> All the best,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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Received on Fri Nov 13 2015 - 14:00:03 PST
