I agree with Dave, and add that using the non-terminal phi/psi terms for
the terminal amino acids (as you suggest in your email) would almost
certainly not be correct, since the charges are very different.
On Mon, Dec 22, 2014 at 8:36 AM, David A Case <case.biomaps.rutgers.edu>
wrote:
>
> On Mon, Dec 15, 2014, nealec wrote:
> >
> > I am confused as to why the Amber force field does not seem to apply a
> > psi dihedral angle to the N-terminal residue of a protein when using a
> > charged N-terminus (nitrogen type N3).
>
> I'm guessing that there is little experimental evidence about psi
> propensities
> for N-terminal residues. Quantum calculations might help, but I don't
> think
> this problem has been attacked in any coordinated way, so Amber force
> fields
> are giving a "default" psi behavior there.
>
> Comments are welcome in case I am missing something.
>
> ...dac
>
>
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Received on Mon Dec 22 2014 - 16:00:03 PST
