Prime User Manual - ISP

100
Chapter 11: Command Syntax
Table 11.6. General keywords for the refinestruct script (Continued)
Keyword syntax Description
SGB_MOD {sgbnp|
vdgbnp}
Prime 2.1 User Manual
Specify the implicit solvation model to use. The choices are:
sgbnp—use the standard generalized Born model.
vdgbnp—use the variable-dielectric generalized Born model, which
uses different dielectric constants based on the polar or charged nature
of the protein residue: 4 for Lys, 3 for Glu/Arg, 2 for Asp/His, 1 for all
others. This method improves loop predictions.
Default: vdgbnp.
STRUCT_FILE filename Input structure file in Maestro format.
USE_CRYSTAL_SYMMETRY
{yes | no}
USE_RANDOM_SEED
{yes | no}
USE_MAE_CHARGES
{yes | no}
USE_MEMBRANE
{yes | no}
Set to true if the input structure contains unit cell information and crystal
symmetric atoms are to be included in calculation. Default: no.
Indicates whether to use a random seed for the random number generator.
This keyword has no effect on Minimization tasks. Default: no.
Indicates whether to use atomic partial charges from the Maestro input
file for untemplated residues (ligands, cofactors). Default: no.
Indicates whether to use the implicit membrane model. The model must
be set up from the Setup Membrane panel in Maestro. Default: no.
USE_SGB {yes | no} Use the SGB implicit solvation model. If the model is not used, calculations
are run in vacuum with a dielectric of 6.0. Default: no.
Table 11.7. Protocol-specific keywords for the refinestruct script
Keyword syntax Description
LOOP_BLD
CA_CONSTRAINT_i
spec,[x,y,z]value
Specify a constraint on the position of a specific alpha carbon atom. The
format of the residue specification spec is given at the beginning of this
chapter. The optional coordinates specify the target position; if omitted,
the target position is the initial position. The value is the maximum distance
that the C-alpha atom can move from the target position, in angstroms.
Specifying a target position allows you to move a loop to a
desired location.
LOOP_i_RES_j spec Specify residue j for defining loop i. Loops are numbered sequentially,
beginning at 0. Two occurrences of this keyword are required, with j=0
(the beginning of the loop) and j=1 (the end of the loop). spec is a residue
specification as defined above.