On Oct 18, 2014, at 5:38 PM, Arun Srikanth <askforarun.gmail.com> wrote:
> Hello amber users,
>
> I used parmed.py to get the impropers for my system. From the discussions
> earlier I understood that the impropers are estimated from bond topology in
> leap based on the definition
>
> " an atom shared by three atoms and all three atoms lie on a plane".
>
> However if I use some other tool to get the list of impropers for my
> system. It differs from what leap assigns ?
I believe that tleap first composes a list of “potential” planar centers that might need an improper by looking for atoms with the right hybridization (e.g., sp2-hybridized carbons).
tleap then looks through the parameter set to see if an improper torsion is defined that matches the atom types involved in that planar center. If no term is found, no improper is assigned -- impropers are not necessarily needed for *every* planar center.
> Can you please explain why is this since both use the same definition of
> impropers. Is it because the tolerance set in estimating whether the three
> atoms are on a plane ?
The criteria is not “are the atoms co-planar” -- the criteria is “does chemical intuition tell you that the atoms _should_ be coplanar”. Parametrization should not depend on the conformation, after all.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Sat Oct 18 2014 - 16:30:03 PDT
