##

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
explicitly.

0pt

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
value of
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
and
were
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
lines:

comment: and for B-B, L-L and L-B, N-L and N-B and N-N
1.0D0 -1.0D0
0.33333333333333D0 0.33333333333333D0
1.0D0 0.0D0
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
LBLBLBLBBNNNBBBLBLBBBNNNLLBLLBBLLBNBLBLBLBLNNNLBBLBLBBBL
EEEEEETEHTHEEEEEEEEHHEHHHHHHHHHHEHTEEEEEEETTTEEEEEEEE

The penultimate line defines the sequence, and the final line
defines which set of , , and parameters apply to which
parts of the structure.[33]

David Wales
2018-06-21