BLN Off-Lattice Protein Model
The general three-colour bead protein model is specified by keyword BLN.
The potential follows the form described in
Proc. Natl. Acad. Sci. USA, 100, 10712, 2003, expect that
the coefficients , , and include a factor of
where is the separation between beads and and
the units of distance and energy are and , respectively.
The first term represents the bonds linking successive beads in the linear chain, and a
was used in most of the work on the
Honeycutt and Thirumalai frustrated 46-bead model.
The second term is a sum over the bond angles, , defined by the triplets
of atomic positions to
, and values
used for the 46-bead model.
The third term
is a sum over the dihedral angles, , defined by the quartets to
In the 46-bead model
if the quartet involved no more than one N monomer, generating
a preference for the trans conformation (
), whereas if two or three
N monomers are involved then and .
This choice makes the three neutral
segments of the chain flexible and enables them to accommodate turns.
A general specification of these parameters is possible in the new BLN framework
via the auxiliary file BLNsequence.
The last term in (3) represents the nonbonded interactions.
In the current BLN implementation is set equal to , i.e. to
unity in reduced units.
An appropriate BLNsequence file for the usual 46-bead model contains the following
comment: and for B-B, L-L and L-B, N-L and N-B and N-N
comment: coefficients A, B, C, D
comment: for Helical, Extended and Turn residues in order, four per line
0.0D0 1.2D0 1.2D0 1.2D0
0.9D0 0.0D0 1.2D0 0.0D0
0.0D0 0.0D0 0.2D0 0.0D0
The penultimate line defines the sequence, and the final line
defines which set of , , and parameters apply to which
parts of the structure.