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

From: David A Case <>
Date: Thu, 24 Sep 2020 11:16:50 -0400

On Wed, Sep 23, 2020, Matias Machado wrote:
>Despite recognising that re-ordering doesn't affect the improper
>definition as long as the central atom is the same, it does generate a
>so called "improper term nightmare" in case of coarse-grained models
>(e.g. SIRAH), which doesn't follow a symmetric phase in 180 as all-atoms
>models do.
>Anyway... in the future I would love to see leap reading the given
>definition instead of doing some re-ordening... that would be much easy
>to understand, develop and transfer...

I'm moving this over to the amber-developers list.

In the really old days, users had to define all the impropers that were
to be used (see the prepin file format). That was deemed to be too
error-prone, so we went over to an algorithmic procedure. But
coarse-graining is clearly a new area. Tleap can read in the
user-defined impropers in prepin files, and (I think) the data is stored
in internal data structures that are not used.

So, it might be all that hard to have a switch to go back to the old
behavior, and allow the coarse-grained folks to define things the way
they need to. The "easy" approach would be limited to the prepin file
format, but that's probably not a major impediment, since antechamber
can convert other file formats to prepin.

I am *not* volunteering here myself, but Scott might be able to provide
some help on the coding side. Or, the CANDO folks might have an
interest here.


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Received on Thu Sep 24 2020 - 08:30:03 PDT
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