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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Received on Thu Mar 24 2016 - 09:30:03 PDT
