How to run rosetta ab initio modeling

Robetta

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Go to: https://www.rosettacommons.org/software/academic/ Username: Academic_User Password: Xry3x4

ab initio

AbinitioRelax.linuxgccrelease -in:file:fasta *.fasta -in:file:frag3 aat000_03_05.200_v1_3 -in:file:frag9 aat000_09_05.200_v1_3 -database /home/yang/software/rosetta/rosetta_database -abinitio:relax -nstruct 1000 -out:pdb -use_filters true -psipred_ss2 *.psipred_ss2 -abinitio::increase_cycles 10 -abinitio::rg_reweight 0.5 -abinitio::rsd_wt_helix 0.5 -abinitio::rsd_wt_loop 0.5 -relax::fast

loop_modeling

loopmodel.linuxgccrelease -in:file:fullatom -in:file:s 3o0g-a_b.pdb -loops:loop_file cdk5.loop_file -loops:frag_sizes 9 3 -loops:frag_files cdk5ex_09_05.200_v1_3 cdk5ex_03_05.200_v1_3 -loops:remodel perturb_ccd -loops:ccd_closure -loops:random_loop -database /home/yang/software/rosetta/rosetta_database/ -mute core.io.database -loops:relax fastrelax -loops:refine refine_kic -loops:extended true -nstruct 1000

Predict Protein-protein Interactions

PPK: docking_prepack_protocol.linuxgccrelease -database /home/yang/software/rosetta/rosetta_database/ -s *.pdb -docking:partners B_A -ignore_unrecognized_res > ppk.log &

LOW: docking_protocol.linuxgccrelease -database /home/yang/software/rosetta/rosetta_database/ -low_res_protocol_only -s 2-22_0001.pdb -docking:partners B_A -spin -dock_pert 3 8 -nstruct 10000 -out:file:scorefile low.sc >low.log &

HIGH: docking_protocol.linuxgccrelease -database /home/yang/software/rosetta/rosetta_database/ -docking_local_refine -s *.pdb -docking:partners B_A -use_input_sc -ex1 -ex2aro -nstruct 10000 &

HIGH_minimization: docking_protocol.linuxgccrelease -database /home/yang/software/rosetta/rosetta_database/ -s *.pdb -docking:partners B_A -ex1 -ex2aro -use_input_sc -no_filters -docking_local_refine -dock_min -mute core.util.prof -out:overwrite -out:file:fullatom -mute core.io.database -nstruct 2000 &

cluster: cluster.linuxgccrelease -database /home/yang/software/rosetta/rosetta_database -in:file:s com*.pdb -out:file:silent_struct_type binary -cluster:radius -1 -score:weights -cluster:sort_groups_by_energy -run:shuffle -nstruct 1 -in:file:fullatom > cluster8.log&

Simple Score calculation

score: score.linuxgccrelease -database /home/yang/software/rosetta/rosetta_database -in:file:s *.pdb -no_optH -ignore_unrecognized_res > score.log&

scons bin mode=release