patches/D_AA.txt patches/CtermProtein.txt patches/NtermProtein.txt patches/disulfide.txt patches/protein_cutpoint_upper.txt patches/protein_cutpoint_lower.txt patches/VirtualBB.txt patches/protein_centroid_with_HA.txt patches/VirtualNterm.txt patches/N_acetylated.txt patches/C_methylamidated.txt patches/RepulsiveOnly_centroid.txt patches/ser_phosphorylated.txt patches/thr_phosphorylated.txt patches/CtermConnect.txt patches/NtermConnect.txt patches/pro_hydroxylated_case1.txt patches/pro_hydroxylated_case2.txt # Command-line selected. patches/ShoveBB.txt ## DNA patches/nucleic/dna/LowerDNA.txt patches/nucleic/dna/UpperDNA.txt patches/nucleic/dna/VirtualDNAPhosphate.txt ## RNA patches/nucleic/rna/LowerRNA.txt patches/nucleic/rna/UpperRNA.txt patches/nucleic/rna/Virtual_Phosphate.txt ##fpd #patches/CtermTruncation.txt #patches/NtermTruncation.txt ## Branching patches patches/branching/C-terminal_conjugation.txt patches/branching/S-linked_conjugation.txt patches/branching/N-linked_conjugation.txt patches/branching/O-linked_conjugation.txt patches/branching/sidechain_carboxyl_conjugation.txt ## carbohydrate patches (These are currently direct copies of the fa patches.) ### termini patches/carbohydrates/lower_terminus.txt patches/carbohydrates/upper_terminus.txt #patches/carbohydrates/Me_glycoside.txt ### cutpoints patches/carbohydrates/cutpoint_lower.txt patches/carbohydrates/cutpoint_upper.txt ### patches/branching (requires -read_pdb_link_records flag to patch) patches/carbohydrates/N-linked_glycosylation.txt patches/carbohydrates/branch_lower_term.txt patches/carbohydrates/2-branch.txt patches/carbohydrates/3-branch.txt patches/carbohydrates/4-branch.txt patches/carbohydrates/6-branch.txt ### modifications patches/carbohydrates/2-amination.txt patches/carbohydrates/3-amination.txt patches/carbohydrates/3-methylation.txt patches/carbohydrates/N-acetyl-2-amination.txt patches/carbohydrates/N-R-3'-hydroxybutyryl-3-amination.txt patches/carbohydrates/5-acetylation.txt #patches/carbohydrates/2-sulfation.txt #patches/carbohydrates/6-sulfation.txt #patches/carbohydrates/2-sulfamidation.txt patches/carbohydrates/omega-oxidation.txt