When comparing prmtop files created by leap (AmberTools 1.4 version) for
GLY and GLY-NHE (where GLY is GLY and not NGLY) with the ff99SB force
field, I found some inconsistencies in the dihedrals:
The HA2-CA-C-O dihedral has a multiplicity of 3 in GLY-NHE whereas
the same dihedral in GLY has a multiplicity of 2, and the HA3-CA-C-O
dihedral in GLY-NHE has a multiplicity of 2.
This is of course inconsistent because: 1) the HA2-CA-C-O dihedral
belongs to the GLY residue and its parameters should not be affected by
the presence of the NHE residue; 2) as HA2 and HA3 atoms are equivalent,
HA2-CA-C-O and HA3-CA-C-O dihedrals should have the same parameters.
It appears that the multiplicity of 2 for the HA2-CA-C-O dihedral
corresponds to the expected H1-CT-C-O parameters in parm99.dat:
H1-CT-C -O 1 0.80 0.0 -1. Junmei et al, 1999
H1-CT-C -O 1 0.08 180.0 3. Junmei et al, 1999
while the multiplicity of 3 corresponds to the addition of the wild-card
parameter:
X -C -CT-X 6 0.00 0.0 2. JCC,7,(1986),230
I was wondering if this problem is known, and what could explain the
inconsistency in the assignment of parameters for this type of dihedral.
Note that the problem also occurs with other GLY-XXX sequences.
--
Thomas Gaillard
Maître de conférences
Laboratoire de Biochimie
Ecole Polytechnique
91128 Palaiseau cedex
tel: +33 1 69 33 48 62
fax: +33 1 69 33 49 09
thomas.gaillard.polytechnique.edu
http://bioc.polytechnique.fr/~gaillard
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu May 19 2011 - 17:30:02 PDT
