Flags for RosettaMP from 2014

Flag Description
-mp:setup:spanfiles <vector of strings> Spanning topology file converted from OCTOPUS output; unless otherwise specified for certain applications, only one should be provided
-mp:setup:spans_from_structure <bool> Uses spanning topology computed from the PDB; requires the protein to be transformed into the membrane coordinate frame!
-mp:setup:lipsfile <string> Lipid accessibility file converted from LIPS output, default=mypdb.lips4
-mp:setup:center <vector of reals> Membrane center x,y,z
-mp:setup:normal <vector of reals> Membrane normal x,y,z
-mp:setup:membrane_rsd <real> Membrane residue number for reading in a PDB file with MEM coordinates
-mp:thickness <real> User-defined membrane thickness. Overwrites default thickness of 60A.
-mp:scoring:hbond <bool> Hydrogen bonding energy correction for membrane proteins
-mp:no_interpolate_Mpair <bool> Advanced scoring parameter from RosettaMembrane; don't interpolate between layers for membrane pair potential
-mp:Hbond_depth_correction <bool> Advanced scoring parameter from RosettaMembrane; correct hydrogen bonds for membrane depth
-mp:TMprojection <bool> Advanced scoring: Penalty for hydrophobic mismatch on/off.
-mp:wt_TMprojection <real> Advanced scoring: Weight for hydrophobic mismatch penalty.
-mp:non_helix <bool> Advanced scoring: Penalty for non-helix residues in the membrane on/off.
-mp:wt_non_helix <real> Advanced scoring: Weight for non-helix penalty.
-mp:termini <bool> Advanced scoring: Penalty for termini in the membrane on/off.
-mp:wt_termini <real> Advanced scoring: Weight for termini penalty.
-mp:secstruct <bool> Advanced scoring: Penalty if structure-based secondary structure doesn\t match predicted one - on/off
-mp:wt_secstruct <real> Advanced scoring: Weight for secondary structure penalty.
-mp:spanning <bool> Advanced scoring: Penalty if structure-based spanning doesn\t match spanfile - on/off.
-mp:wt_spanning <real> Advanced scoring: Weight for spanning penalty.
-mp:viewer:thickness <real> PyMOL plugin: Thickness of membrane to visualize, default=15
-mp:viewer:num_points <int> PyMOL plugin: Number of points to define the membrane planes. x >= 3
-mp:visualize:embedding <bool> VisualizeEmbedddingMover: Visualize embedding centers and normals for each TMspan
-mp:visualize:spacing <real> VisualizeMembraneMover: Spacing of virtual membrane residues representing the membrane planes, default=5
-mp:visualize:width <real> VisualizeMembraneMover: Width of membrane planes for n by n plane, default=100
-mp:visualize:thickness <real> VisualizeMembraneMover: Thickness of membrane to visualize, default=15
-mp:visualize:plane_radius <real> VisualizeMembraneMover: Radius of membrane planes to draw in PyMol - part of the PyMol viewer plugin

Flags for RosettaMembrane from 2006 (will be deprecated soon)

Flag Description
-membrane Initialize a pose as a membrane pose
-in:file:spanfile Spanfile containing transmembrane span information, converted from OCTOPUS output
-in:file:lipofile Lipophilicity file containing lipid accessibilities, converted from LIPS output
-center_search Perform membrane center search, default false
-normal search Perform membrane normal search, default false
-center_mag Magnitude of membrane normal center search (Angstroms), default 1
-center_max_delta Magnitude of maximum membrane width deviation during membrane center search (Angstroms), default 5
-normal_start_angle magnitude of starting angle during membrane normal search (degrees), default 10
-normal_delta_angle magnitude of angle deviation during membrane normal search (degrees), default 10
-normal_cycles Cycles for finding good embedding normal, default 100
-normal_max_angle magnitude of maximum angle deviation during membrane normal search (degrees), default 40
-normal_mag Magnitude of membrane normal angle search (degrees), default 5
-smooth_move_frac ???, default 0.5
-no_interpolate_Mpair Don't interpolate between layers for pair interactions, default false
-Menv_penalties Turn on penalties, default false
-Mhbond_depth Membrane depth dependent correction to the hbond potential, default false
-Membed_init ??? default false
-Fa_Membed_update ??? default false
-fixed_membrane Fix membrane position, by default the center is at [0,0,0] and membrane normal is the z-axis, default false
-membrane_center Membrane center x,y,z
-membrane_normal Membrane normal x,y,z
-thickness One leaflet hydrocarbon thickness for solvation calculations (Angstroms), default 15
-view View membrane during protocol, default false
-debug Print debug output, default false

References

Alford RF, Koehler Leman J, Weitzner BD, Duran A, Tiley DC, Gray JJ (2015). An integrated framework advancing membrane protein modeling and design. PLoS Comput. Biol. - In Press

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