rosettaCM_flags2018

-database /opt/rosetta_2018.09.60072/main/database 
# i/o
-in:file:fasta Outputs/Alignments/Target_RTM.fasta 
-parser:protocol Config/rosettaCM_2018.xml 
-nstruct 100
-out:level 100 

-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 
-sog_upper_bound 15 
-overwrite 

# 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