It seems that conjugated polymers which involve five membered ring
structures is not modelled very well.
I will look in to the suggestions
Thank you very much
Arun
On Tue, Oct 24, 2017 at 8:09 AM, David A Case <david.case.rutgers.edu>
wrote:
> On Mon, Oct 23, 2017, Arun Srikanth wrote:
> >
> > I used parmchk2 to get the parameters for my molecule.
> > But one of the dihedral parameters has a high penalty score.
> >
> > Is there any way to correct this
> >
> > cd-cc-os-cc 2 2.100 180.000 2.000 same as X
> > -c2-os-X , penalty score=232.0
>
> The high "penalty" means that the required parameter is not very close to
> one that has been parameterized, and this indeed looks like an odd
> combination. "Correccting" this would involve checking what the force
> field
> predicts compared to quantum calculations (or to experimental data if you
> have
> it.) Amber's "paramfit" program is one way to approach such comparisons,
> and
> is generally pretty easy to use. Others on the list may have their own
> favorite approaches, and are welcome to chime in here.
>
> ...dac
>
>
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Received on Tue Oct 24 2017 - 07:30:05 PDT
