[ bondedtypes ]
; Col 1: Type of bond
; Col 2: Type of angles
; Col 3: Type of proper dihedrals
; Col 4: Type of improper dihedrals
; Col 5: Generate all dihedrals if 1, only heavy atoms of 0.
; Col 6: Number of excluded neighbors for nonbonded interactions
; Col 7: Generate 1,4 interactions between pairs of hydrogens if 1
; Col 8: Remove propers over the same bond as an improper if it is 1
; bonds angles dihedrals impropers all_dihedrals nrexcl HH14 RemoveDih
    1       5       9       2       1       3       1       0
[ ALA ]
    [ atoms ]
        N       NH1     -0.47   0
        HN      H        0.31   1
        CA      CT1      0.07   2
        HA      HB       0.09   3
        CB      CT3     -0.27   4
        HB1     HA       0.09   5
        HB2     HA       0.09   6
        HB3     HA       0.09   7
        C       C        0.51   8
        O       O       -0.51   9
    [ bonds ]
        CB      CA
        N       HN
        N       CA
        C       CA
        C       +N
        CA      HA
        CB      HB1
        CB      HB2
        CB      HB3
        O       C
    [ impropers ]
        N       -C      CA      HN
        C       CA      +N      O
[ ARG ]
    [ atoms ]
        N       NH1     -0.47    0
        HN      H        0.31    1
        CA      CT1      0.07    2
        HA      HB       0.09    3
        CB      CT2     -0.18    4
        HB1     HA       0.09    5
        HB2     HA       0.09    6
        CG      CT2     -0.18    7
        HG1     HA       0.09    8
        HG2     HA       0.09    9
        CD      CT2      0.20   10
        HD1     HA       0.09   11
        HD2     HA       0.09   12
        NE      NC2     -0.61   13  ; CHARMM22*
        HE      HC       0.38   14  ; CHARMM22*
        CZ      C        0.49   15  ; CHARMM22*
        NH1     NC2     -0.62   16  ; CHARMM22*
        HH11    HC       0.40   17  ; CHARMM22*
        HH12    HC       0.40   18  ; CHARMM22*
        NH2     NC2     -0.62   19  ; CHARMM22*
        HH21    HC       0.40   20  ; CHARMM22*
        HH22    HC       0.40   21  ; CHARMM22*
        C       C        0.51   22
        O       O       -0.51   23
    [ bonds ]
        CB      CA
        CG      CB
        CD      CG
        NE      CD
        CZ      NE
        NH2     CZ
        N       HN
        N       CA
        C       CA
        C       +N
        CA      HA
        CB      HB1
        CB      HB2
        CG      HG1
        CG      HG2
        CD      HD1
        CD      HD2
        NE      HE
        NH1     HH11
        NH1     HH12
        NH2     HH21
        NH2     HH22
        O       C
        CZ      NH1
    [ impropers ]
        N       -C      CA      HN
        C       CA      +N      O
        CZ      NH1     NH2     NE
[ ASN ]
    [ atoms ]
        N       NH1     -0.47    0
        HN      H        0.31    1
        CA      CT1      0.07    2
        HA      HB       0.09    3
        CB      CT2     -0.18    4
        HB1     HA       0.09    5
        HB2     HA       0.09    6
        CG      CC       0.55    7
        OD1     O       -0.55    8
        ND2     NH2     -0.62    9
        HD21    H        0.32   10
        HD22    H        0.30   11
        C       C       0.51    12
        O       O       -0.51   13
    [ bonds ]
        CB      CA
        CG      CB
        ND2     CG
        N       HN
        N       CA
        C       CA
        C       +N
        CA      HA
        CB      HB1
        CB      HB2
        ND2     HD21
        ND2     HD22
        C       O
        CG      OD1
    [ impropers ]
        N       -C      CA      HN
        C       CA      +N      O
        CG      ND2     CB      OD1
        CG      CB      ND2     OD1
        ND2     CG      HD21    HD22
        ND2     CG      HD22    HD21
[ ASP ]
    [ atoms ]
        N       NH1     -0.47    0
        HN      H        0.31    1
        CA      CT1      0.07    2
        HA      HB       0.09    3
        CB      CT2     -0.28    4  ; CHARMM22*
        HB1     HA       0.05    5  ; CHARMM22*
        HB2     HA       0.05    6  ; CHARMM22*
        CG      CC       0.56    7  ; CHARMM22*
        OD1     OC      -0.69    8  ; CHARMM22*
        OD2     OC      -0.69    9  ; CHARMM22*
        C       C        0.51   10
        O       O       -0.51   11
    [ bonds ]
        CB      CA
        CG      CB
        OD2     CG
        N       HN
        N       CA
        C       CA
        C       +N
        CA      HA
        CB      HB1
        CB      HB2
        O       C
        CG      OD1
    [ impropers ]
        N       -C      CA      HN
        C       CA      +N      O
        CG      CB      OD2     OD1
[ ASPP ] ; protonated ASP
    [ atoms ]
        N       NH1     -0.47    0
        HN      H        0.31    1
        CA      CT1      0.07    2
        HA      HB       0.09    3
        CB      CT2     -0.21    4  ;
        HB1     HA       0.09    5  ; HB1 OD1
        HB2     HA       0.09    6  ; | //
        CG      CD       0.75    7  ; -CB--CG
        OD1     OB      -0.55    8  ; | \
        OD2     OH1     -0.61    9  ; HB2 OD2-HD2
        HD2     H        0.44   10  ;
        C       C        0.51   11
        O       O       -0.51   12
    [ bonds ]
        CB      CA
        CG      CB
        OD2     CG
        OD2     HD2
        N       HN
        N       CA
        C       CA
        C       +N
        CA      HA
        CB      HB1
        CB      HB2
        O       C
        CG      OD1
    [ impropers ]
        N       -C      CA      HN
        C       CA      +N      O
        CG      CB      OD2     OD1
[ CYS ]
    [ atoms ]
        N       NH1     -0.47    0
        HN      H        0.31    1
        CA      CT1      0.07    2
        HA      HB       0.09    3
        CB      CT2     -0.11    4
        HB1     HA       0.09    5
        HB2     HA       0.09    6
        SG      S       -0.23    7
        HG1     HS       0.16    8
        C       C        0.51    9
        O       O       -0.51   10
    [ bonds ]
        CB      CA
        SG      CB
        N       HN
        N       CA
        C       CA
        C       +N
        CA      HA
        CB      HB1
        CB      HB2
        SG      HG1
        O       C
    [ impropers ]
        N       -C      CA      HN
        C       CA      +N      O
[ CYS2 ] ; disulfide cystine
    [ atoms ]
        N       NH1     -0.47    0
        HN      H        0.31    1
        CA      CT1      0.07    2
        HA      HB       0.09    3
        CB      CT2     -0.10    4
        HB1     HA       0.09    5
        HB2     HA       0.09    6
        SG      SM      -0.08    7
        C       C        0.51    8
        O       O       -0.51    9
    [ bonds ]
        CB      CA
        SG      CB
        N       HN
        N       CA
        C       CA
        C       +N
        CA      HA
        CB      HB1
        CB      HB2
        O       C
    [ impropers ]
        N       -C      CA      HN
        C       CA      +N      O
[ GLN ]
    [ atoms ]
        N       NH1     -0.47    0
        HN      H        0.31    1
        CA      CT1      0.07    2
        HA      HB       0.09    3
        CB      CT2     -0.18    4
        HB1     HA       0.09    5
        HB2     HA       0.09    6
        CG      CT2     -0.18    7
        HG1     HA       0.09    8
        HG2     HA       0.09    9
        CD      CC       0.55   10
        OE1     O       -0.55   11
        NE2     NH2     -0.62   12
        HE21    H        0.32   13
        HE22    H        0.30   14
        C       C        0.51   15
        O       O       -0.51   16
    [ bonds ]
        CB      CA
        CG      CB
        CD      CG
        NE2     CD
        N       HN
        N       CA
        C       CA
        C       +N
        CA      HA
        CB      HB1
        CB      HB2
        CG      HG1
        CG      HG2
        NE2     HE21
        NE2     HE22
        O       C
        CD      OE1
    [ impropers ]
        N       -C      CA      HN
        C       CA      +N      O
        CD      NE2     CG      OE1
        CD      CG      NE2     OE1
        NE2     CD      HE21    HE22
        NE2     CD      HE22    HE21
[ GLU ]
    [ atoms ]
        N       NH1     -0.47    0
        HN      H        0.31    1
        CA      CT1      0.07    2
        HA      HB       0.09    3
        CB      CT2     -0.18    4
        HB1     HA       0.09    5
        HB2     HA       0.09    6
        CG      CT2     -0.28    7  ; CHARMM22*
        HG1     HA       0.05    8  ; CHARMM22*
        HG2     HA       0.05    9  ; CHARMM22*
        CD      CC       0.56   10  ; CHARMM22*
        OE1     OC      -0.69   11  ; CHARMM22*
        OE2     OC      -0.69   12  ; CHARMM22*
        C       C        0.51   13
        O       O       -0.51   14
    [ bonds ]
        CB      CA
        CG      CB
        CD      CG
        OE2     CD
        N       HN
        N       CA
        C       CA
        C       +N
        CA      HA
        CB      HB1
        CB      HB2
        CG      HG1
        CG      HG2
        O       C
        CD      OE1
    [ impropers ]
        N       -C      CA      HN
        C       CA      +N      O
        CD      CG      OE2     OE1
[ GLUP ] ; protonated GLU
    [ atoms ]
        N       NH1     -0.47    0
        HN      H        0.31    1
        CA      CT1      0.07    2
        HA      HB       0.09    3
        CB      CT2     -0.18    4
        HB1     HA       0.09    5
        HB2     HA       0.09    6
        CG      CT2     -0.21    7  ;
        HG1     HA       0.09    8  ; HG1 OE1
        HG2     HA       0.09    9  ; | //
        CD      CD       0.75   10  ; -CG--CD
        OE1     OB      -0.55   11  ; |       \
        OE2     OH1     -0.61   12  ; HG2     OE2-HE2
        HE2     H        0.44   13  ;
        C       C        0.51   14
        O       O       -0.51   15
    [ bonds ]
        CB      CA
        CG      CB
        CD      CG
        OE2     CD
        OE2     HE2
        N       HN
        N       CA
        C       CA
        C       +N
        CA      HA
        CB      HB1
        CB      HB2
        CG      HG1
        CG      HG2
        O       C
        CD      OE1
    [ impropers ]
        N       -C      CA      HN
        C       CA      +N      O
        CD      CG      OE2     OE1
[ GLY ]
    [ atoms ]
        N       NH1     -0.47    0
        HN      H        0.31    1
        CA      CT2     -0.02    2
        HA1     HB       0.09    3
        HA2     HB       0.09    4
        C       C        0.51    5
        O       O       -0.51    6
    [ bonds ]
        N       HN
        N       CA
        C       CA
        C       +N
        CA      HA1
        CA      HA2
        O       C
    [ impropers ]
        N       -C      CA      HN
        C       CA      +N      O
    [ cmap ]
        -C      N       CA      C       +N
[ HSD ]
    [ atoms ]
        N       NH1     -0.47    0
        HN      H        0.31    1
        CA      CT1      0.07    2
        HA      HB       0.09    3
        CB      CT2     -0.09    4
        HB1     HA       0.09    5
        HB2     HA       0.09    6
        ND1     NR1     -0.36    7
        HD1     H        0.32    8
        CG      CPH1    -0.05    9
        CE1     CPH2     0.25   10
        HE1     HR1      0.13   11
        NE2     NR2     -0.70   12
        CD2     CPH1     0.22   13
        HD2     HR3      0.10   14
        C       C        0.51   15
        O       O       -0.51   16
    [ bonds ]
        CB      CA
        CG      CB
        ND1     CG
        CE1     ND1
        NE2     CD2
        N       HN
        N       CA
        C       CA
        C       +N
        CA      HA
        CB      HB1
        CB      HB2
        ND1     HD1
        CD2     HD2
        CE1     HE1
        O       C
        CG      CD2
        CE1     NE2
    [ impropers ]
        ND1     CG      CE1     HD1
        CD2     CG      NE2     HD2
        CE1     ND1     NE2     HE1
        ND1     CE1     CG      HD1
        CD2     NE2     CG      HD2
        CE1     NE2     ND1     HE1
        N       -C      CA      HN
        C       CA      +N      O
[ HSE ]
    [ atoms ]
        N       NH1     -0.47    0
        HN      H        0.31    1
        CA      CT1      0.07    2
        HA      HB       0.09    3
        CB      CT2     -0.08    4
        HB1     HA       0.09    5
        HB2     HA       0.09    6
        ND1     NR2     -0.70    7
        CG      CPH1     0.22    8
        CE1     CPH2     0.25    9
        HE1     HR1      0.13   10
        NE2     NR1     -0.36   11
        HE2     H        0.32   12
        CD2     CPH1    -0.05   13
        HD2     HR3      0.09   14
        C       C        0.51   15
        O       O       -0.51   16
    [ bonds ]
        CB      CA
        CG      CB
        ND1     CG
        NE2     CD2
        N       HN
        N       CA
        C       CA
        C       +N
        NE2     CE1
        CA      HA
        CB      HB1
        CB      HB2
        NE2     HE2
        CD2     HD2
        CE1     HE1
        O       C
        CD2     CG
        CE1     ND1
    [ impropers ]
        NE2     CD2     CE1     HE2
        CD2     CG      NE2     HD2
        CE1     ND1     NE2     HE1
        NE2     CE1     CD2     HE2
        CD2     NE2     CG      HD2
        CE1     NE2     ND1     HE1
        N       -C      CA      HN
        C       CA      +N      O
[ HSP ]
    [ atoms ]
        N       NH1     -0.47    0
        HN      H        0.31    1
        CA      CT1      0.07    2
        HA      HB       0.09    3
        CB      CT2     -0.05    4
        HB1     HA       0.09    5
        HB2     HA       0.09    6
        CD2     CPH1     0.19    7
        HD2     HR1      0.13    8
        CG      CPH1     0.19    9
        NE2     NR3     -0.51   10
        HE2     H        0.44   11
        ND1     NR3     -0.51   12
        HD1     H        0.44   13
        CE1     CPH2     0.32   14
        HE1     HR2      0.18   15
        C       C        0.51   16
        O       O       -0.51   17
    [ bonds ]
        CB      CA
        CG      CB
        ND1     CG
        CE1     ND1
        NE2     CD2
        N       HN
        N       CA
        C       CA
        C       +N
        CA      HA
        CB      HB1
        CB      HB2
        ND1     HD1
        NE2     HE2
        CD2     HD2
        CE1     HE1
        O       C
        CD2     CG
        NE2     CE1
    [ impropers ]
        ND1     CG      CE1     HD1
        ND1     CE1     CG      HD1
        NE2     CD2     CE1     HE2
        NE2     CE1     CD2     HE2
        N       -C      CA      HN
        C       CA      +N      O
[ ILE ]
    [ atoms ]
        N       NH1     -0.47    0
        HN      H        0.31    1
        CA      CT1      0.07    2
        HA      HB       0.09    3
        CB      CT1     -0.09    4
        HB      HA       0.09    5
        CG2     CT3     -0.27    6
        HG21    HA       0.09    7
        HG22    HA       0.09    8
        HG23    HA       0.09    9
        CG1     CT2     -0.18   10
        HG11    HA       0.09   11
        HG12    HA       0.09   12
        CD      CT3     -0.27   13
        HD1     HA       0.09   14
        HD2     HA       0.09   15
        HD3     HA       0.09   16
        C       C        0.51   17
        O       O       -0.51   18
    [ bonds ]
        CB      CA
        CG1     CB
        CG2     CB
        CD      CG1
        N       HN
        N       CA
        C       CA
        C       +N
        CA      HA
        CB      HB
        CG1     HG11
        CG1     HG12
        CG2     HG21
        CG2     HG22
        CG2     HG23
        CD      HD1
        CD      HD2
        CD      HD3
        O       C
    [ impropers ]
        N       -C      CA      HN
        C       CA      +N      O
[ LEU ]
    [ atoms ]
        N       NH1     -0.47    0
        HN      H        0.31    1
        CA      CT1      0.07    2
        HA      HB       0.09    3
        CB      CT2     -0.18    4
        HB1     HA       0.09    5
        HB2     HA       0.09    6
        CG      CT1     -0.09    7
        HG      HA       0.09    8
        CD1     CT3     -0.27    9
        HD11    HA       0.09   10
        HD12    HA       0.09   11
        HD13    HA       0.09   12
        CD2     CT3     -0.27   13
        HD21    HA       0.09   14
        HD22    HA       0.09   15
        HD23    HA       0.09   16
        C       C        0.51   17
        O       O       -0.51   18
    [ bonds ]
        CB      CA
        CG      CB
        CD1     CG
        CD2     CG
        N       HN
        N       CA
        C       CA
        C       +N
        CA      HA
        CB      HB1
        CB      HB2
        CG      HG
        CD1     HD11
        CD1     HD12
        CD1     HD13
        CD2     HD21
        CD2     HD22
        CD2     HD23
        O       C
    [ impropers ]
        N       -C      CA      HN
        C       CA      +N      O
[ LYS ]
    [ atoms ]
        N       NH1     -0.47    0
        HN      H        0.31    1
        CA      CT1      0.07    2
        HA      HB       0.09    3
        CB      CT2     -0.18    4
        HB1     HA       0.09    5
        HB2     HA       0.09    6
        CG      CT2     -0.18    7
        HG1     HA       0.09    8
        HG2     HA       0.09    9
        CD      CT2     -0.18   10
        HD1     HA       0.09   11
        HD2     HA       0.09   12
        CE      CT2      0.21   13
        HE1     HA       0.05   14
        HE2     HA       0.05   15
        NZ      NH3     -0.30   16
        HZ1     HC       0.33   17
        HZ2     HC       0.33   18
        HZ3     HC       0.33   19
        C       C        0.51   20
        O       O       -0.51   21
    [ bonds ]
        CB      CA
        CG      CB
        CD      CG
        CE      CD
        NZ      CE
        N       HN
        N       CA
        C       CA
        C       +N
        CA      HA
        CB      HB1
        CB      HB2
        CG      HG1
        CG      HG2
        CD      HD1
        CD      HD2
        CE      HE1
        CE      HE2
        O       C
        NZ      HZ1
        NZ      HZ2
        NZ      HZ3
    [ impropers ]
        N       -C      CA      HN
        C       CA      +N      O
[ LSN ] ; neutral lysine residue
    [ atoms ]
        N       NH1     -0.47    0
        HN      H        0.31    1
        CA      CT1      0.07    2
        HA      HB       0.09    3
        CB      CT2     -0.18    4
        HB1     HA       0.09    5
        HB2     HA       0.09    6
        CG      CT2     -0.18    7
        HG1     HA       0.09    8
        HG2     HA       0.09    9
        CD      CT2     -0.18   10
        HD1     HA       0.09   11
        HD2     HA       0.09   12
        CE      CT2      0.13   13
        HE1     HA       0.075  14
        HE2     HA       0.075  15
        NZ      NH2     -0.96   16
        HZ1     HC       0.34   17
        HZ2     HC       0.34   18
        C       C        0.51   19
        O       O       -0.51   20
    [ bonds ]
        CB      CA
        CG      CB
        CD      CG
        CE      CD
        NZ      CE
        N       HN
        N       CA
        C       CA
        C       +N
        CA      HA
        CB      HB1
        CB      HB2
        CG      HG1
        CG      HG2
        CD      HD1
        CD      HD2
        CE      HE1
        CE      HE2
        O       C
        NZ      HZ1
        NZ      HZ2
    [ impropers ]
        N       -C      CA      HN
        C       CA      +N      O
[ MET ]
    [ atoms ]
        N       NH1     -0.47    0
        HN      H        0.31    1
        CA      CT1      0.07    2
        HA      HB       0.09    3
        CB      CT2     -0.18    4
        HB1     HA       0.09    5
        HB2     HA       0.09    6
        CG      CT2     -0.14    7
        HG1     HA       0.09    8
        HG2     HA       0.09    9
        SD      S       -0.09   10
        CE      CT3     -0.22   11
        HE1     HA       0.09   12
        HE2     HA       0.09   13
        HE3     HA       0.09   14
        C       C        0.51   15
        O       O       -0.51   16
    [ bonds ]
        CB      CA
        CG      CB
        SD      CG
        CE      SD
        N       HN
        N       CA
        C       CA
        C       +N
        CA      HA
        CB      HB1
        CB      HB2
        CG      HG1
        CG      HG2
        CE      HE1
        CE      HE2
        CE      HE3
        O       C
    [ impropers ]
        N       -C      CA      HN
        C       CA      +N      O
[ PHE ]
    [ atoms ]
        N       NH1     -0.47    0
        HN      H        0.31    1
        CA      CT1      0.07    2
        HA      HB       0.09    3
        CB      CT2     -0.18    4
        HB1     HA       0.09    5
        HB2     HA       0.09    6
        CG      CA       0.00    7
        CD1     CA      -0.115   8
        HD1     HP       0.115   9
        CE1     CA      -0.115  10
        HE1     HP       0.115  11
        CZ      CA      -0.115  12
        HZ      HP       0.115  13
        CD2     CA      -0.115  14
        HD2     HP       0.115  15
        CE2     CA      -0.115  16
        HE2     HP       0.115  17
        C       C        0.51   18
        O       O       -0.51   19
    [ bonds ]
        CB      CA
        CG      CB
        CD2     CG
        CE1     CD1
        CZ      CE2
        N       HN
        N       CA
        C       CA
        C       +N
        CA      HA
        CB      HB1
        CB      HB2
        CD1     HD1
        CD2     HD2
        CE1     HE1
        O       C
        CD1     CG
        CZ      CE1
        CE2     CD2
        CE2     HE2
        CZ      HZ
    [ impropers ]
        N       -C      CA      HN
        C       CA      +N      O
[ PRO ]
    [ atoms ]
        N       N       -0.29    0
        CD      CP3      0.00    1
        HD1     HA       0.09    2
        HD2     HA       0.09    3
        CA      CP1      0.02    4
        HA      HB       0.09    5
        CB      CP2     -0.18    6
        HB1     HA       0.09    7
        HB2     HA       0.09    8
        CG      CP2     -0.18    9
        HG1     HA       0.09   10
        HG2     HA       0.09   11
        C       C        0.51   12
        O       O       -0.51   13
    [ bonds ]
        C       CA
        C       +N
        N       CA
        CA      CB
        CB      CG
        CG      CD
        N       CD
        HA      CA
        HG1     CG
        HG2     CG
        HD1     CD
        HD2     CD
        HB1     CB
        HB2     CB
        O       C
    [ impropers ]
        N       -C      CA      CD
        C       CA      +N      O
    [ cmap ]
        -C      N       CA      C       +N
[ SER ]
    [ atoms ]
        N       NH1     -0.47    0
        HN      H        0.31    1
        CA      CT1      0.07    2
        HA      HB       0.09    3
        CB      CT2      0.05    4
        HB1     HA       0.09    5
        HB2     HA       0.09    6
        OG      OH1     -0.66    7
        HG1     H        0.43    8
        C       C        0.51    9
        O       O       -0.51   10
    [ bonds ]
        CB      CA
        OG      CB
        N       HN
        N       CA
        C       CA
        C       +N
        CA      HA
        CB      HB1
        CB      HB2
        OG      HG1
        O       C
    [ impropers ]
        N       -C      CA      HN
        C       CA      +N      O
[ THR ]
    [ atoms ]
        N       NH1     -0.47    0
        HN      H        0.31    1
        CA      CT1      0.07    2
        HA      HB       0.09    3
        CB      CT1      0.14    4
        HB      HA       0.09    5
        OG1     OH1     -0.66    6
        HG1     H        0.43    7
        CG2     CT3     -0.27    8
        HG21    HA       0.09    9
        HG22    HA       0.09   10
        HG23    HA       0.09   11
        C       C        0.51   12
        O       O       -0.51   13
    [ bonds ]
        CB      CA
        OG1     CB
        CG2     CB
        N       HN
        N       CA
        C       CA
        C       +N
        CA      HA
        CB      HB
        OG1     HG1
        CG2     HG21
        CG2     HG22
        CG2     HG23
        O       C
    [ impropers ]
        N       -C      CA      HN
        C       CA      +N      O
[ TRP ]
    [ atoms ]
        N       NH1     -0.47    0
        HN      H        0.31    1
        CA      CT1      0.07    2
        HA      HB       0.09    3
        CB      CT2     -0.18    4
        HB1     HA       0.09    5
        HB2     HA       0.09    6
        CG      CY      -0.03    7
        CD1     CA       0.035   8
        HD1     HP       0.115   9
        NE1     NY      -0.61   10
        HE1     H        0.38   11
        CE2     CPT      0.13   12
        CD2     CPT     -0.02   13
        CE3     CA      -0.115  14
        HE3     HP       0.115  15
        CZ3     CA      -0.115  16
        HZ3     HP       0.115  17
        CZ2     CA      -0.115  18
        HZ2     HP       0.115  19
        CH2     CA      -0.115  20
        HH2     HP       0.115  21
        C       C        0.51   22
        O       O       -0.51   23
    [ bonds ]
        CB      CA
        CG      CB
        CD2     CG
        NE1     CD1
        CZ2     CE2
        N       HN
        N       CA
        C       CA
        C       +N
        CZ3     CH2
        CD2     CE3
        NE1     CE2
        CA      HA
        CB      HB1
        CB      HB2
        CD1     HD1
        NE1     HE1
        CE3     HE3
        CZ2     HZ2
        CZ3     HZ3
        CH2     HH2
        O       C
        CD1     CG
        CE2     CD2
        CZ3     CE3
        CH2     CZ2
    [ impropers ]
        N       -C      CA      HN
        C       CA      +N      O
[ TYR ]
    [ atoms ]
        N       NH1     -0.47    0
        HN      H        0.31    1
        CA      CT1      0.07    2
        HA      HB       0.09    3
        CB      CT2     -0.18    4
        HB1     HA       0.09    5
        HB2     HA       0.09    6
        CG      CA       0.00    7
        CD1     CA      -0.115   8
        HD1     HP       0.115   9
        CE1     CA      -0.115  10
        HE1     HP       0.115  11
        CZ      CA       0.11   12
        OH      OH1     -0.54   13
        HH      H        0.43   14
        CD2     CA      -0.115  15
        HD2     HP       0.115  16
        CE2     CA      -0.115  17
        HE2     HP       0.115  18
        C       C        0.51   19
        O       O       -0.51   20
    [ bonds ]
        CB      CA
        CG      CB
        CD2     CG
        CE1     CD1
        CZ      CE2
        OH      CZ
        N       HN
        N       CA
        C       CA
        C       +N
        CA      HA
        CB      HB1
        CB      HB2
        CD1     HD1
        CD2     HD2
        CE1     HE1
        CE2     HE2
        OH      HH
        O       C
        CD1     CG
        CE1     CZ
        CE2     CD2
    [ impropers ]
        N       -C      CA      HN
        C       CA      +N      O
[ VAL ]
    [ atoms ]
        N       NH1     -0.47    0
        HN      H        0.31    1
        CA      CT1      0.07    2
        HA      HB       0.09    3
        CB      CT1     -0.09    4
        HB      HA       0.09    5
        CG1     CT3     -0.27    6
        HG11    HA       0.09    7
        HG12    HA       0.09    8
        HG13    HA       0.09    9
        CG2     CT3     -0.27   10
        HG21    HA       0.09   11
        HG22    HA       0.09   12
        HG23    HA       0.09   13
        C       C        0.51   14
        O       O       -0.51   15
    [ bonds ]
        CB      CA
        CG1     CB
        CG2     CB
        N       HN
        N       CA
        C       CA
        C       +N
        CA      HA
        CB      HB
        CG1     HG11
        CG1     HG12
        CG1     HG13
        CG2     HG21
        CG2     HG22
        CG2     HG23
        O       C
    [ impropers ]
        N       -C      CA      HN
        C       CA      +N      O
[ ALAD ] ; Alanine dipeptide
    [ atoms ]
        CL      CT3     -0.27    0
        HL1     HA       0.09    1
        HL2     HA       0.09    2
        HL3     HA       0.09    3
        CLP     C        0.51    4
        OL      O       -0.51    5
        NL      NH1     -0.47    6
        HL      H        0.31    7
        CA      CT1      0.07    8
        HA      HB       0.09    9
        CB      CT3     -0.27   10
        HB1     HA       0.09   11
        HB2     HA       0.09   12
        HB3     HA       0.09   13
        CRP     C        0.51   14
        OR      O       -0.51   15
        NR      NH1     -0.47   16
        HR      H        0.31   17
        CR      CT3     -0.11   18
        HR1     HA       0.09   19
        HR2     HA       0.09   20
        HR3     HA       0.09   21
    [ bonds ]
        CL      CLP
        CLP     NL
        NL      CA
        CA      CRP
        CRP     NR
        NR      CR
        CLP     OL
        CRP     OR
        NL      HL
        NR      HR
        CA      HA
        CA      CB
        CL      HL1
        CL      HL2
        CL      HL3
        CB      HB1
        CB      HB2
        CB      HB3
        CR      HR1
        CR      HR2
        CR      HR3
    [ impropers ]
        CLP     CL      NL      OL
        NL      CLP     CA      HL
        CRP     CA      NR      OR
        NR      CRP     CR      HR
[ HEME ]
    [ atoms ]
        FE      FE       0.24    0
        NA      NPH     -0.18    1
        NB      NPH     -0.18    2
        NC      NPH     -0.18    3
        ND      NPH     -0.18    4
        C1A     CPA      0.12    5
        C2A     CPB     -0.06    6
        C3A     CPB     -0.06    7
        C4A     CPA      0.12    8
        C1B     CPA      0.12    9
        C2B     CPB     -0.06   10
        C3B     CPB     -0.06   11
        C4B     CPA      0.12   12
        C1C     CPA      0.12   13
        C2C     CPB     -0.06   14
        C3C     CPB     -0.06   15
        C4C     CPA      0.12   16
        C1D     CPA      0.12   17
        C2D     CPB     -0.06   18
        C3D     CPB     -0.06   19
        C4D     CPA      0.12   20
        CHA     CPM     -0.10   21
        HA      HA       0.10   22
        CHB     CPM     -0.10   23
        HB      HA       0.10   24
        CHC     CPM     -0.10   25
        HC      HA       0.10   26
        CHD     CPM     -0.10   27
        HD      HA       0.10   28
        CMA     CT3     -0.27   29
        HMA1    HA       0.09   30
        HMA2    HA       0.09   31
        HMA3    HA       0.09   32
        CAA     CT2     -0.18   33
        HAA1    HA       0.09   34
        HAA2    HA       0.09   35
        CBA     CT2     -0.28   36
        HBA1    HA       0.09   37
        HBA2    HA       0.09   38
        CGA     CC       0.62   39
        O1A     OC      -0.76   40
        O2A     OC      -0.76   41
        CMB     CT3     -0.27   42
        HMB1    HA       0.09   43
        HMB2    HA       0.09   44
        HMB3    HA       0.09   45
        CAB     CE1     -0.15   46
        HAB     HE1      0.15   47
        CBB     CE2     -0.42   48
        HBB1    HE2      0.21   49
        HBB2    HE2      0.21   50
        CMC     CT3     -0.27   51
        HMC1    HA       0.09   52
        HMC2    HA       0.09   53
        HMC3    HA       0.09   54
        CAC     CE1     -0.15   55
        HAC     HE1      0.15   56
        CBC     CE2     -0.42   57
        HBC1    HE2      0.21   58
        HBC2    HE2      0.21   59
        CMD     CT3     -0.27   60
        HMD1    HA       0.09   61
        HMD2    HA       0.09   62
        HMD3    HA       0.09   63
        CAD     CT2     -0.18   64
        HAD1    HA       0.09   65
        HAD2    HA       0.09   66
        CBD     CT2     -0.28   67
        HBD1    HA       0.09   68
        HBD2    HA       0.09   69
        CGD     CC       0.62   70
        O1D     OC      -0.76   71
        O2D     OC      -0.76   72
    [ bonds ]
        FE      NA
        FE      NB
        FE      NC
        FE      ND
        NA      C1A
        C1A     C2A
        C2A     C3A
        C3A     C4A
        NA      C4A
        C2A     CAA
        CAA     CBA
        CBA     CGA
        CGA     O1A
        CGA     O2A
        C3A     CMA
        CHB     C4A
        CHB     C1B
        NB      C1B
        C1B     C2B
        C2B     C3B
        C3B     C4B
        NB      C4B
        C2B     CMB
        C3B     CAB
        CAB     CBB
        CHC     C4B
        CHC     C1C
        NC      C1C
        C1C     C2C
        C2C     C3C
        C3C     C4C
        NC      C4C
        C2C     CMC
        C3C     CAC
        CAC     CBC
        CHD     C4C
        CHD     C1D
        ND      C1D
        C1D     C2D
        C2D     C3D
        C3D     C4D
        ND      C4D
        C2D     CMD
        C3D     CAD
        CAD     CBD
        CBD     CGD
        CGD     O1D
        CGD     O2D
        CHA     C4D
        CHA     C1A
        CHA     HA
        CHB     HB
        CHC     HC
        CHD     HD
        CAA     HAA1
        CAA     HAA2
        CBA     HBA1
        CBA     HBA2
        CMA     HMA1
        CMA     HMA2
        CMA     HMA3
        CMB     HMB1
        CMB     HMB2
        CMB     HMB3
        CAB     HAB
        CBB     HBB1
        CBB     HBB2
        CMC     HMC1
        CMC     HMC2
        CMC     HMC3
        CAC     HAC
        CBC     HBC1
        CBC     HBC2
        CMD     HMD1
        CMD     HMD2
        CMD     HMD3
        CAD     HAD1
        CAD     HAD2
        CBD     HBD1
        CBD     HBD2
    [ angles ]
; ai aj ak th0 cth ub0 cub
        NA      FE      NC      180.0   0.0     0.0     0.0
        NB      FE      ND      180.0   0.0     0.0     0.0
    [ impropers ]
        C2A     C1A     C3A     CAA
        C3A     C2A     C4A     CMA
        C2B     C1B     C3B     CMB
        C3B     C2B     C4B     CAB
        C2C     C1C     C3C     CMC
        C3C     C2C     C4C     CAC
        C2D     C1D     C3D     CMD
        C3D     C2D     C4D     CAD
        CGA     CBA     O2A     O1A
        CGD     CBD     O2D     O1D
        C4A     NA      C1A     C2A
        C1A     NA      C4A     C3A
        C4B     NB      C1B     C2B
        C1B     NB      C4B     C3B
        C4C     NC      C1C     C2C
        C1C     NC      C4C     C3C
        C4D     ND      C1D     C2D
        C1D     ND      C4D     C3D
        NA      C1A     C2A     C3A
        NA      C4A     C3A     C2A
        NB      C1B     C2B     C3B
        NB      C4B     C3B     C2B
        NC      C1C     C2C     C3C
        NC      C4C     C3C     C2C
        ND      C1D     C2D     C3D
        ND      C4D     C3D     C2D
        NA      C1A     CHA     C4D
        NA      C4A     CHB     C1B
        NB      C1B     CHB     C4A
        NB      C4B     CHC     C1C
        NC      C1C     CHC     C4B
        NC      C4C     CHD     C1D
        ND      C1D     CHD     C4C
        ND      C4D     CHA     C1A
        CHA     C1A     C4D     HA
        CHB     C1B     C4A     HB
        CHC     C1C     C4B     HC
        CHD     C1D     C4C     HD
        C1A     C2A     CHA     NA
        C4A     C3A     CHB     NA
        C1B     C2B     CHB     NB
        C4B     C3B     CHC     NB
        C1C     C2C     CHC     NC
        C4C     C3C     CHD     NC
        C1D     C2D     CHD     ND
        C4D     C3D     CHA     ND
        NA      C1A     C4A     FE
        NB      C1B     C4B     FE
        NC      C1C     C4C     FE
        ND      C1D     C4D     FE
[ HEO2 ]
    [ atoms ]
        FE      FE       0.24    0
        NA      NPH     -0.18    1
        NB      NPH     -0.18    2
        NC      NPH     -0.18    3
        ND      NPH     -0.18    4
        C1A     CPA      0.12    5
        C2A     CPB     -0.06    6
        C3A     CPB     -0.06    7
        C4A     CPA      0.12    8
        C1B     CPA      0.12    9
        C2B     CPB     -0.06   10
        C3B     CPB     -0.06   11
        C4B     CPA      0.12   12
        C1C     CPA      0.12   13
        C2C     CPB     -0.06   14
        C3C     CPB     -0.06   15
        C4C     CPA      0.12   16
        C1D     CPA      0.12   17
        C2D     CPB     -0.06   18
        C3D     CPB     -0.06   19
        C4D     CPA      0.12   20
        CHA     CPM     -0.10   21
        HA      HA       0.10   22
        CHB     CPM     -0.10   23
        HB      HA       0.10   24
        CHC     CPM     -0.10   25
        HC      HA       0.10   26
        CHD     CPM     -0.10   27
        HD      HA       0.10   28
        CMA     CT3     -0.27   29
        HMA1    HA       0.09   30
        HMA2    HA       0.09   31
        HMA3    HA       0.09   32
        CAA     CT2     -0.18   33
        HAA1    HA       0.09   34
        HAA2    HA       0.09   35
        CBA     CT2     -0.28   36
        HBA1    HA       0.09   37
        HBA2    HA       0.09   38
        CGA     CC       0.62   39
        O1A     OC      -0.76   40
        O2A     OC      -0.76   41
        CMB     CT3     -0.27   42
        HMB1    HA       0.09   43
        HMB2    HA       0.09   44
        HMB3    HA       0.09   45
        CAB     CE1     -0.15   46
        HAB     HE1      0.15   47
        CBB     CE2     -0.42   48
        HBB1    HE2      0.21   49
        HBB2    HE2      0.21   50
        CMC     CT3     -0.27   51
        HMC1    HA       0.09   52
        HMC2    HA       0.09   53
        HMC3    HA       0.09   54
        CAC     CE1     -0.15   55
        HAC     HE1      0.15   56
        CBC     CE2     -0.42   57
        HBC1    HE2      0.21   58
        HBC2    HE2      0.21   59
        CMD     CT3     -0.27   60
        HMD1    HA       0.09   61
        HMD2    HA       0.09   62
        HMD3    HA       0.09   63
        CAD     CT2     -0.18   64
        HAD1    HA       0.09   65
        HAD2    HA       0.09   66
        CBD     CT2     -0.28   67
        HBD1    HA       0.09   68
        HBD2    HA       0.09   69
        CGD     CC       0.62   70
        O1D     OC      -0.76   71
        O2D     OC      -0.76   72
        O1      OM       0.021  73
        O2      OM      -0.021  74
    [ bonds ]
        FE      NA
        FE      NB
        FE      NC
        FE      ND
        NA      C1A
        C1A     C2A
        C2A     C3A
        C3A     C4A
        NA      C4A
        C2A     CAA
        CAA     CBA
        CBA     CGA
        CGA     O1A
        CGA     O2A
        C3A     CMA
        CHB     C4A
        CHB     C1B
        NB      C1B
        C1B     C2B
        C2B     C3B
        C3B     C4B
        NB      C4B
        C2B     CMB
        C3B     CAB
        CAB     CBB
        CHC     C4B
        CHC     C1C
        NC      C1C
        C1C     C2C
        C2C     C3C
        C3C     C4C
        NC      C4C
        C2C     CMC
        C3C     CAC
        CAC     CBC
        CHD     C4C
        CHD     C1D
        ND      C1D
        C1D     C2D
        C2D     C3D
        C3D     C4D
        ND      C4D
        C2D     CMD
        C3D     CAD
        CAD     CBD
        CBD     CGD
        CGD     O1D
        CGD     O2D
        CHA     C4D
        CHA     C1A
        CHA     HA
        CHB     HB
        CHC     HC
        CHD     HD
        CAA     HAA1
        CAA     HAA2
        CBA     HBA1
        CBA     HBA2
        CMA     HMA1
        CMA     HMA2
        CMA     HMA3
        CMB     HMB1
        CMB     HMB2
        CMB     HMB3
        CAB     HAB
        CBB     HBB1
        CBB     HBB2
        CMC     HMC1
        CMC     HMC2
        CMC     HMC3
        CAC     HAC
        CBC     HBC1
        CBC     HBC2
        CMD     HMD1
        CMD     HMD2
        CMD     HMD3
        CAD     HAD1
        CAD     HAD2
        CBD     HBD1
        CBD     HBD2
        O1      O2
        O1      FE
    [ angles ]
; ai aj ak th0 cth ub0 cub
        NA      FE      NC      180.0   0.0     0.0     0.0
        NB      FE      ND      180.0   0.0     0.0     0.0
        FE      O1      O2      122.0   50.00   0.0     0.0
    [ impropers ]
        C2A     C1A     C3A     CAA
        C3A     C2A     C4A     CMA
        C2B     C1B     C3B     CMB
        C3B     C2B     C4B     CAB
        C2C     C1C     C3C     CMC
        C3C     C2C     C4C     CAC
        C2D     C1D     C3D     CMD
        C3D     C2D     C4D     CAD
        CGA     CBA     O2A     O1A
        CGD     CBD     O2D     O1D
        C4A     NA      C1A     C2A
        C1A     NA      C4A     C3A
        C4B     NB      C1B     C2B
        C1B     NB      C4B     C3B
        C4C     NC      C1C     C2C
        C1C     NC      C4C     C3C
        C4D     ND      C1D     C2D
        C1D     ND      C4D     C3D
        NA      C1A     C2A     C3A
        NA      C4A     C3A     C2A
        NB      C1B     C2B     C3B
        NB      C4B     C3B     C2B
        NC      C1C     C2C     C3C
        NC      C4C     C3C     C2C
        ND      C1D     C2D     C3D
        ND      C4D     C3D     C2D
        NA      C1A     CHA     C4D
        NA      C4A     CHB     C1B
        NB      C1B     CHB     C4A
        NB      C4B     CHC     C1C
        NC      C1C     CHC     C4B
        NC      C4C     CHD     C1D
        ND      C1D     CHD     C4C
        ND      C4D     CHA     C1A
        CHA     C1A     C4D     HA
        CHB     C1B     C4A     HB
        CHC     C1C     C4B     HC
        CHD     C1D     C4C     HD
        C1A     C2A     CHA     NA
        C4A     C3A     CHB     NA
        C1B     C2B     CHB     NB
        C4B     C3B     CHC     NB
        C1C     C2C     CHC     NC
        C4C     C3C     CHD     NC
        C1D     C2D     CHD     ND
        C4D     C3D     CHA     ND
        NA      C1A     C4A     FE
        NB      C1B     C4B     FE
        NC      C1C     C4C     FE
        ND      C1D     C4D     FE
[ O2 ] ; O2 ligand for HEME
    [ atoms ]
        O1      OM       0.021   0
        O2      OM      -0.021   1
    [ bonds ]
        O1      O2
[ CO ] ; CO ligand for HEME
    [ atoms ]
        C       CM       0.021   0
        O       OM      -0.021   1
    [ bonds ]
        C       O
[ HOH ]
    [ atoms ]
        OW      OT      -0.834   0
        HW1     HT       0.417   1
        HW2     HT       0.417   2
    [ bonds ]
        OW      HW1
        OW      HW2
        HW1     HW2
[ TIP3 ]
    [ atoms ]
        OH2     OT      -0.834   0
        H1      HT       0.417   1
        H2      HT       0.417   2
    [ bonds ]
        OH2     H1
        OH2     H2
        H1      H2
[ TP3M ]
    [ atoms ]
        OH2     OT      -0.834   0
        H1      HT       0.417   1
        H2      HT       0.417   2
    [ bonds ]
        OH2     H1
        OH2     H2
[ SOD ]
    [ atoms ]
        SOD     SOD      1.00    0
[ MG ]
    [ atoms ]
        MG      MG       2.00    0
[ POT ]
    [ atoms ]
        POT     POT      1.00    0
[ CES ]
    [ atoms ]
        CES     CES      1.00    0
[ CAL ]
    [ atoms ]
        CAL     CAL      2.00    0
[ CLA ]
    [ atoms ]
        CLA     CLA     -1.00    0
[ ZN2 ]
    [ atoms ]
        ZN      ZN       2.00    0

[ ACE ]
 [ atoms ]
        CH3     CT3     -0.270  0
        HH31    HA      0.090   1
        HH32    HA      0.090   2
        HH33    HA      0.090   3
        C       C       0.510   4
        O       O       -0.510  5
 [ bonds ]
        C       CH3
        C       +N
        CH3     HH31
        CH3     HH32
        CH3     HH33
        O       C
 [ impropers ]
        C       CH3     +N      O

[ CT3 ]
; this can also be done with the .c.tdb, but the atom naming is different
; and this can matter
 [ atoms ]
        N       NH1     -0.470  0
        HN      H       0.310   1
        CH3     CT3     -0.110  2
        HH31    HA      0.090   3
        HH32    HA      0.090   4
        HH33    HA      0.090   5
 [ bonds ]
        -C      N
        N       HN
        N       CH3
        CH3     HH31
        CH3     HH32
        CH3     HH33

 [ impropers ]
        N       -C      CH3     HN
        -C      CH3     N       -O
