protein relax

[Anonymous]

I am trying to relax my protein with ligands FMN before do further design. I used movemap to exclude the rotamer on FMN. my flag and movemap file looks like below. I also attached my protein_FMN pdb. It takes an extremely long time and it seems like stuck somewhere (I attached the screen shot). Is it normal and anybody knows why? Thanks

flag file:

-in:file:s ./input/3TX9.A_FMN_Crystal.pdb

-in:file:movemap movemapfile

# Harmonic runs

-relax:constrain_relax_to_start_coords

-relax:ramp_constraints false

-relax:coord_constrain_sidechains

-relax:coord_cst_stdev 0.5

-out:path:pdb ./output

-out:path:score ./score

-out:suffix _harmonicrelax

-nstruct 1

 

movemalfile

RESIDUE * BBCHI

RESIDUE 400 NO

JUMP 1 YES

 

program stuck at this position: 

basic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat

core.scoring.elec.util: Read 40 countpair representative atoms

core.pack.dunbrack.RotamerLibrary: shapovalov_lib_fixes_enable option is true.

core.pack.dunbrack.RotamerLibrary: shapovalov_lib::shap_dun10_smooth_level of 1( aka lowest_smooth ) got activated.

core.pack.dunbrack.RotamerLibrary: Binary rotamer library selected: /home/apps/software/rosetta/3.12-IGB-gcc-4.9.4/main/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin

core.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file ‘/home/apps/software/rosetta/3.12-IGB-gcc-4.9.4/main/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin’.

core.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.25 seconds to load from binary

core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_FMN

core.pack.pack_rotamers: built 1 rotamers at 1 positions.

core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph

protocols.relax.FastRelax: CMD: repeat  5715.89  0  0  0.55

protocols.relax.FastRelax: CMD: coord_cst_weight  5715.89  0  0  0.55

protocols.relax.FastRelax: CMD: scale:fa_rep  -597.19  0  0  0.022

core.pack.task: Packer task: initialize from command line() 

core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_FMN

core.pack.pack_rotamers: built 5343 rotamers at 400 positions.

core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph

protocols.relax.FastRelax: CMD: repack  -767.647  0  0  0.022

protocols.relax.FastRelax: CMD: scale:fa_rep  -694.876  0  0  0.02805

(stuck here for a long time)

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