# i/o -in:file:fasta /Users/kulkarnik/Research/Rosetta_2014/rosettahmmer/gadd45g/gadd45g.fasta -nstruct 20 -parser:protocol rosetta_cm.xml -out:file:silent_struct_type binary # 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_rlx.wts -use_bicubic_interpolation -hybridize:stage1_probability 1.0 -sog_upper_bound 15 # 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