Team:NAWI Graz/Model/rosetta bash

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Unix terminal commands to run Rosetta3CM protocol

$rosetta stands for your installation path, for example /home/rosetta/

$rosetta/bin/partial_thread.default.linuxgccrelease -in:file:fasta 2_threading/targetprotein(g17).fasta -in:file:alignment example1.grishin -in:file:template_pdb example1.pdb

$rosetta/main/source/bin/rosetta_scripts.default.linuxgccrelease @rosetta_cm.options

$rosetta/main/source/bin/relax.default.linuxgccrelease @relax.options

Content of rosetta_cm.options

# i/o
-in:file:fasta g17.fasta
-parser:protocol rosetta_cm.xml
-nstruct X #intended number X of constructs to be produced

# relax options
-relax:minimize_bond_angles
-relax:minimize_bond_lengths
-relax:jump_move true
-default_max_cycles 200
-relax:min_type lbfgs_armijo_nonmonotone
-relax:jump_move true
-score:weights stage3.wts
-use_bicubic_interpolation
-hybridize:stage1_probability 1.0

# reduce memory footprint
-chemical:exclude_patches LowerDNA UpperDNA Cterm_amidation SpecialRotamer VirtualBB ShoveBB VirtualDNAPhosphate VirtualNTerm CTermConnect sc_orbitals pro_hydroxylated_case1 pro_hydroxylated_case2 ser_phosphorylated thr_phosphorylated tyr_phosphorylated tyr_sulfated lys_dimethylated lys_monomethylated lys_trimethylated lys_acetylated glu_carboxylated cys_acetylated tyr_diiodinated N_acetylated C_methylamidated MethylatedProteinCterm

Content of rosetta_cm.xml

<ROSETTASCRIPTS>><br> <TASKOPERATIONS><br> </TASKOPERATIONS><br> <SCOREFXNS><br> <ScoreFunction name="stage1" weights="stage1.wts" symmetric="0"><br> <Reweight scoretype="atom_pair_constraint" weight="1"/><br> </ScoreFunction><br> <ScoreFunction name="stage2" weights="stage2.wts" symmetric="0"><br> <Reweight scoretype="atom_pair_constraint" weight="0.5"/><br> </ScoreFunction><br> <ScoreFunction name="fullatom" weights="stage3.wts" symmetric="0"><br> <Reweight scoretype="atom_pair_constraint" weight="0.5"/><br> </ScoreFunction><br> </SCOREFXNS><br> <FILTERS><br> </FILTERS><br> <MOVERS><br> <Hybridize name="hybridize" stage1_scorefxn="stage1" stage2_scorefxn="stage2" fa_scorefxn="fullatom" batch="1" stage1_increase_cycles="1.0" stage2_increase_cycles="1.0" linmin_only="1"><br> <Fragments three_mers="g17_3.frags" nine_mers="g17_9.frags"/><br> <Template pdb="g17_on_6gw0.pdb" cst_file="AUTO" weight="1.000" /><br> <Template pdb="g17_on_5m5z.pdb" cst_file="AUTO" weight="1.000" /><br> <Template pdb="g17_on_4l9b.pdb" cst_file="AUTO" weight="1.000" /><br> <Template pdb="g17_on_5xqgA.pdb" cst_file="AUTO" weight="1.000" /><br> </Hybridize><br> </MOVERS><br> <APPLY_TO_POSE><br> </APPLY_TO_POSE><br> <PROTOCOLS><br> <Add mover="hybridize"/><br> </PROTOCOLS><br><br> </ROSETTASCRIPTS>

Content of rosetta_cm.options

-score:weights ref2015.wts

-relax:dualspace #use dualspace relax protocol
-relax:minimize_bond_angles #dualspace relax protocol setting
-set_weights cart_bonded .5 pro_close 0 #score proline ring closure using energy term for all bond lengths (pro_close uses virtual atom NV for proline ring scores)
-default_max_cycles 200

-out:file:fullatom
-out:pdb