Change the CG definitions

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Below is a sample file format for the CG definitions:

  {
    "ALA":["[N,CA,C,O,CB]","[r1_0,r1_0,r1_0,r1_0,r8_0]"],
    "ARG":["[N,CA,C,O,CB,CG,CD,NE,NH1,NH2,CZ]","[r1_0,r1_0,r1_0,r1_0,r2_0,r2_1,r3_0,r3_0,r3_0,r3_0,r3_0]"],
    "ASN":["[N,CA,C,O,CB,CG,ND2,OD1]","[r1_0,r1_0,r1_0,r1_0,r2_0,r9_0,r9_0,r9_0]"],
    "ASP":["[N,CA,C,O,CB,CG,OD1,OD2]","[r1_0,r1_0,r1_0,r1_0,r6_0,r6_0,r6_0,r6_0]"],
    "CYS":["[N,CA,C,O,CB,SG]","[r1_0,r1_0,r1_0,r1_0,r10_0,r10_0]"],
    "GLN":["[N,CA,C,O,CB,CG,CD,NE2,OE1]","[r1_0,r1_0,r1_0,r1_0,r2_0,r2_1,r9_0,r9_0,r9_0]"],
    "GLU":["[N,CA,C,O,CB,CG,CD,OE1,OE2]","[r1_0,r1_0,r1_0,r1_0,r2_0,r6_0,r6_0,r6_0,r6_0]"],
    "GLY":["[N,CA,C,O]","[r1_0,r1_0,r1_0,r1_0]"],
    "HIS":["[N,CA,C,O,CB,CG,CD2,ND1,CE1,NE2]","[r1_0,r1_0,r1_0,r1_0,r4_0,r4_0,r4_0,r4_0,r4_0,r4_0]"],
    "ILE":["[N,CA,C,O,CB,CG1,CG2,CD1]","[r1_0,r1_0,r1_0,r1_0,r12_0,r2_0,r8_0,r8_1]"],
    "LEU":["[N,CA,C,O,CB,CG,CD1,CD2]","[r1_0,r1_0,r1_0,r1_0,r2_0,r12_0,r8_0,r8_1]"],
    "LYS":["[N,CA,C,O,CB,CG,CD,CE,NZ]","[r1_0,r1_0,r1_0,r1_0,r2_0,r2_1,r2_2,r5_0,r5_0]"],
    "MET":["[N,CA,C,O,CB,SD,CE]","[r1_0,r1_0,r1_0,r1_0,r13_0,r13_0,r13_0]"],
    "PHE":["[N,CA,C,O,CB,CG,CD1,CD2,CE1,CE2,CZ]","[r1_0,r1_0,r1_0,r1_0,r2_0,r14_0,r14_0,r14_0,r14_0,r14_0,r14_0]"],
    "PRO":["[N,CA,C,O,CB,CG,CD]","[r11_0,r11_0,r11_0,r11_0,r11_0,r11_0,r11_0]"],
    "SER":["[N,CA,C,O,CB,OG]","[r1_0,r1_0,r1_0,r1_0,r7_0,r7_0]"],
    "THR":["[N,CA,C,O,CB,OG1,CG2]","[r1_0,r1_0,r1_0,r1_0,r7_0,r7_0,r8_0]"],
    "TRP":["[N,CA,C,O,CB,CG,CD1,CD2,NE1,CE2,CE3,CH2,CZ2,CZ3]","[r1_0,r1_0,r1_0,r1_0,r2_0,r15_0,r15_0,r15_0,r15_0,r15_0,r15_0,r15_0,r15_0,r15_0]"],
    "TYR":["[N,CA,C,O,CB,CG,CD1,CD2,CE1,CE2,CZ,OH]","[r1_0,r1_0,r1_0,r1_0,r2_0,r16_0,r16_0,r16_0,r16_0,r16_0,r16_0,r16_0]"],
    "VAL":["[N,CA,C,O,CB,CG1,CG2]","[r1_0,r1_0,r1_0,r1_0,r12_0,r8_0,r8_1]"]
  }

Here the atom labels can be changed to ignore atoms and the cg name should always be of type r#1_#2 where #1 is the type of CG and #2 is used to differentiate different occurences of the same CG in an amino acid. Not including '_#2' defaults the occurence number to 0, i.e. r1 is the same as r1_0

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