How to run rosetta ab initio modeling

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Revision as of 19:50, 24 September 2019 by Wu3857 (talk | contribs) (Created page with "==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/rose...")
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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

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