More on docking flags
See the docking quick
reference card (located in the RosettaDock parent directory) for a
detailed description
of all Rosetta flags.
Protocol flags:
-dock_min: minimize the full-atom decoy
-dock_mcm: Monte Carlo minimize the full-atom decoy
-prepack_full: separate the components, repack separately, put
them back, and write PDB (to create starting position)
-prepack_rtmin: prepack_full, with off-rotamer sampling of side
chains added
Overall docking flags (I
frequently refer to these as "search flags"):
-randomize1:
randomize orientation of partner 1
-randomize2:
randomize orientation of partner 2
-spin:
spin the partners randomly around line of centers
(automatically on if randomize 1 or 2 is on)
-dock_pert
<n> <p> <r>: initial perturbation of
the starting structure
n: normal
perturbation in
angstroms (along the line of centers; default = 3.0 A)
p:
parallel perturbation
in angstroms (in the plane perpendicular to the line of centers;
default = 8.0A)
r:
rotational perturbation in deg (both rotation relative to the
line
of centers and rotation around the line of centers; default = 8 deg)
Side chain modeling flags:
The default protocol for chi angles is to model three standard rotamers
per angle. The -ex flags model the three standard angles and each
of
the three standard angles plus or minus one standard deviation, for a
total of nine rotamers per angle. If -ex is turned on for all
four chi
angles, the simulation time will become very long. We suggest
using
just -ex1 and -ex2aro_only.
-ex1: use
extra conformations (nine rotamers) for chi1 angles in side-chain
packing
-ex2:
use extra conformations for chi2 angles in side-chain packing
-ex3:
use extra conformations for chi3 angles in side-chain packing
-ex4:
use extra conformations for chi4 angles in side-chain packing
-ex2aro_only:
use extra rotamers for only TRP,PHE and TYR chi2 angles in
side-chain packing
-find_disulf:
treat cysteine side-chains in a disulfide bond specially
-norepack_disulf:
do not change cysteine side-chain conformations if
in a disulfide bond (need -find_disulf to be functional)
-norepack1:
do not change side-chain conformations in the protein partner 1
-norepack2:
do not change side-chain conformations in the protein partner
-unboundrot:
add original side-chain angles from the "unbound"
structure into the rotamer library for side-chain packing (require the
unbound structure to be defined)
-dock_rtmin
allow off-rotamer side-chain modeling during docking
fullatom "dock_mcm" mode. (In prepacking step, use -prepack_rtmin, else use -prepack_full).
dock_pert is best used for optimizing an already good structure or
for sampling the energy surface around a correct ('native') structure.
The dock_rtmin option is described in detail in
Wang et al., Protein Science 2005.
Again, randomize is best used in a blind run. You can randomize
one partner or both. If no randomize flag is given, the default
is dock_pert 3 8 8. If you are confident that the interface is
confined to a certain patch on a docking partner, then you will want to
orient that patch toward the interface before docking and NOT randomize
that partner.
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