Hi Cody,
For the second part of your question, you're right that the input
conformation won't necessarily have the equilibrium values for lengths and
angles. However, you provide several input structures to paramfit, and the
goal is that the force field parameters generated by the program will be
robust enough to provide accurate energies for positions that are not at
the exact equilibrium.
You may get better results if you give paramfit input structures and QM
energies that have been optimized with the desired dihedral fixed,
especially if there are steric clashes when you force rotation about the
dihedral. However, this is not necessary for the program's function, as
paramfit calculates the MM energy of each input structure with the input
parameters, and adjusts the parameters so that the MM energy matches the QM
energy. The idea is that over a set of structures the resulting adjustments
will produce a maximally correct set of parameters no matter how the
molecule is positioned.
The parameter K is to account for the fact that in simulations forces (the
gradient of the energy) are used rather than energies. K is a constant term
that disappears when taking the gradient, but is necessary to add in to
make the energies fit to zero.
I hope this makes more sense- let me know if it doesn't.
Robin Betz
On Thu, Apr 18, 2013 at 10:42 AM, Covington, Cody Lance <
cody.l.covington.vanderbilt.edu> wrote:
> Hi
>
> I was looking into the paramfit program to get a few dihedral parameters,
> and had a few questions that I haven't found answers to in the manual or
> mailing list.
>
>
> 1) The molecule I am parameterizing has 60 atoms so I was going to
> try a smaller fragment. Since electrostatic interactions are calculated in
> 1-4 interactions, are there any considerations for RESP charges? I could
> use the entire molecule and lower the basis set.
>
> 2) The Amber force field will have a different set of equilibrium
> bond lengths and angles than the QM calculations. Is this accounted for in
> the 'K' term? Shouldn't a geometry optimization be performed in amber with
> the ff with the dihedral angle fixed, then a QM optimization calculation
> with the dihedral angle fixed? From the examples in the manual, it looks
> like the energies are just calculated using both MM and QM and compared.
> Any help would be appreciated!
>
> Thanks
> Cody
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>
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Received on Thu Apr 18 2013 - 17:00:02 PDT
