Indeed, CN and CB are the two atoms that join the two rings in TRP. (and
in purines both of these atoms are type CB) -- Thanks Dave!
On Thu, Mar 24, 2016 at 12:00 PM, David A Case <david.case.rutgers.edu>
wrote:
> On Thu, Mar 24, 2016, Brent Krueger wrote:
>
> > While we are here talking about impropers, can someone explain to me why
> we
> > leave two of the improper dihedrals in TRP undefined (C*-CN-CB-CA
> > and NA-CA-CN-CB)? I presume this is obvious to some in the group and
> that
> > they are just unnecessary because things stay appropriately planar
> without
> > them, but I've always been curious about this.
>
> Are these the impropers around the two atoms that are common to both rings
> in
> TRP? We found out back in 1986 (see the first all-atom force field paper)
> that the out-of-plane vibrational frequencies could be matched rather well
> without including those impropers (i.e. by setting their force constants to
> zero). Same thing for the briding atoms in purines, as I recall. Might be
> worth re-visiting now that we have better quantum mechanics. (Not sure
> what
> ff14ipq does with this...)
>
> ...dac
>
>
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--
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Brent P. Krueger.....................phone: 616 395 7629
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Received on Thu Mar 24 2016 - 09:30:10 PDT
