[AMBER] Missing psi dihedral at cationic N-terminus of protein/peptide?

From: nealec <nealec.rpi.edu>
Date: Mon, 15 Dec 2014 16:32:42 -0500

Dear Users:

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). For example, in
amber14/dat/leap/parm/parm99.dat , I find the psi dihedral definition
for non-N-terminal residues:

N -CT-C -N 1 1.700 180.000 -1.
N -CT-C -N 1 2.000 180.000 2.

But there are no corresponding values including N3 and it appears that
in this case the following null dihedral will be used:

X -C -CT-X 6 0.00 0.0 2.

The psi dihedrals (N -CT-C -N) seem to have been added at some point
after the 1986 paper to reduce alpha-helical character, but I don't see
any special mention of discounting a psi including type N3 in the
Cornell 1995 JACS paper, the Kollman 1996 Acc. Chem. Res. paper, or the
Wang 2000 J. Comp. Chem paper. However, in Wang 2000 J. Comp. Chem. on
page 1067, it does explicitly show that N-C-C-N dihedrals were
redefined; that this N-C-C-N dihedral is referred to by element, not by
amber atom-type, suggests that these dihedrals should apply also to the
N3 atom type, although the tests in that paper with the alanine di- and
tetra-peptides would I believe not have had an N3 atom type, so perhaps
it is ambiguous.

Could this be a force-field oversight or am I missing something?

Thank you,

AMBER mailing list
Received on Mon Dec 15 2014 - 14:00:02 PST
Custom Search