/usr/share/gromacs/top/encadv.ff/aminoacids.rtp is in gromacs-data 4.6.5-1build1.
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1822 1823 1824 1825 1826 1827 1828 1829 1830 1831 1832 1833 1834 1835 1836 1837 1838 1839 1840 1841 1842 1843 1844 1845 1846 1847 1848 1849 1850 1851 1852 1853 1854 1855 1856 1857 1858 1859 1860 1861 1862 1863 1864 1865 1866 1867 1868 1869 1870 1871 1872 1873 1874 1875 1876 1877 1878 1879 1880 1881 1882 1883 1884 1885 1886 1887 1888 1889 1890 1891 1892 1893 1894 1895 1896 1897 1898 1899 1900 1901 1902 1903 1904 1905 1906 1907 1908 1909 1910 1911 1912 1913 1914 1915 1916 1917 1918 1919 1920 1921 1922 1923 1924 1925 1926 1927 1928 1929 1930 1931 1932 1933 1934 1935 1936 1937 1938 1939 1940 1941 1942 1943 1944 1945 1946 1947 1948 1949 1950 1951 1952 1953 1954 1955 1956 1957 1958 1959 1960 1961 1962 1963 1964 1965 1966 1967 1968 1969 1970 1971 1972 1973 1974 1975 1976 1977 1978 1979 1980 1981 1982 | ;
; Encad residue topology file.
; Note that this is only a subset of all molecules described
; in Encad. If you need to use a new one, it might help to
; study the parameter files of Encad.
;
[ bondedtypes ]
; Column 1 : default bondtype
; Column 2 : default angletype
; Column 3 : default proper dihedraltype
; Column 4 : default improper dihedraltype
; Column 5 : This controls the generation of dihedrals from the bonding.
; All possible dihedrals are generated automatically. A value of
; 1 here means that all these are retained. A value of
; 0 here requires generated dihedrals be removed if
; * there are any dihedrals on the same central atoms
; specified in the residue topology, or
; * there are other identical generated dihedrals
; sharing the same central atoms, or
; * there are other generated dihedrals sharing the
; same central bond that have fewer hydrogen atoms
; Column 6 : number of neighbors to exclude from non-bonded interactions
; Column 7 : 1 = generate 1,4 interactions between pairs of hydrogen atoms
; 0 = do not generate such
; Column 8 : 1 = remove proper dihedrals if found centered on the same
; bond as an improper dihedral
; 0 = do not generate such
; bonds angles dihedrals impropers all_dihedrals nrexcl bHH14 bRemoveDih
1 1 1 1 0 3 1
[ ACE ]
[ atoms ]
CH3 C3 -0.357 1
HH31 H 0.119 1
HH32 H 0.119 1
HH33 H 0.119 1
C Aprime 0.380 2
O O -0.380 2
[ bonds ]
CH3 HH31
CH3 HH32
CH3 HH33
CH3 C
C O
[ dihedrals ]
HH33 CH3 C +N
CH3 C +N +CA
[ impropers ]
C HH33 CH3 HH31 improper_X_X_C_X
C HH33 CH3 HH32 improper_X_X_C_X
CH3 +N C O improper_X_X_A_X
[ ALA ]
[ atoms ]
N N1 -0.333 0
H HN 0.333 0
CA C1 -0.119 1
HA H 0.119 1
CB C3 -0.357 2
HB1 H 0.119 2
HB2 H 0.119 2
HB3 H 0.119 2
C Aprime 0.380 3
O O -0.380 3
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB HB3
C O
-C N
[ dihedrals ]
-CA -C N CA
-C N CA C
N CA CB HB3
N CA C +N
[ impropers ]
-C CA N H improper_X_X_N_X
N C CA HA improper_X_X_C_X
N C CA CB improper_N_A_C1_C
CA HB3 CB HB1 improper_X_X_C_X
CA HB3 CB HB2 improper_X_X_C_X
CA +N C O improper_X_X_A_X
[ ARG ]
[ atoms ]
N N1 -0.333 0
H HN 0.333 0
CA C1 -0.119 1
HA H 0.119 1
CB C2 -0.238 2
HB1 H 0.119 2
HB2 H 0.119 2
CG C2 -0.238 3
HG1 H 0.119 3
HG2 H 0.119 3
CD C2 -0.238 4
HD1 H 0.119 4
HD2 H 0.119 4
NE M1 -0.333 5
HE HN 0.333 5
CZ A6 0.000 6
NH1 M2 -0.666 7
HH11 HN 0.383 7
HH12 HN 0.383 7
NH2 M2 -0.666 8
HH21 HN 0.383 8
HH22 HN 0.383 8
C Aprime 0.380 9
O O -0.380 9
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB CG
CG HG1
CG HG2
CG CD
CD HD1
CD HD2
CD NE
NE HE
NE CZ
CZ NH1
CZ NH2
NH1 HH11
NH1 HH12
NH2 HH21
NH2 HH22
C O
-C N
[ dihedrals ]
-CA -C N CA
-C N CA C
N CA CB CG
N CA C +N
CA CB CG CD
CB CG CD NE
CG CD NE CZ
CD NE CZ NH2
NE CZ NH1 HH12
NE CZ NH2 HH22
[ impropers ]
-C CA N H improper_X_X_N_X
N C CA HA improper_X_X_C_X
N C CA CB improper_N_A_C1_C
CA +N C O improper_X_X_A_X
CA CG CB HB1 improper_X_X_C_X
CA CG CB HB2 improper_X_X_C_X
CB CD CG HG1 improper_X_X_C_X
CB CD CG HG2 improper_X_X_C_X
CG NE CD HD1 improper_X_X_C_X
CG NE CD HD2 improper_X_X_C_X
CD CZ NE HE improper_X_X_M_X
NE NH2 CZ NH1 improper_X_X_A_X
CZ HH12 NH1 HH11 improper_X_X_M_X
CZ HH22 NH2 HH21 improper_X_X_M_X
[ ARGN ]
[ atoms ]
N N1 -0.333 0
H HN 0.333 0
CA C1 -0.119 1
HA H 0.119 1
CB C2 -0.238 2
HB1 H 0.119 2
HB2 H 0.119 2
CG C2 -0.238 3
HG1 H 0.119 3
HG2 H 0.119 3
CD C2 -0.238 4
HD1 H 0.119 4
HD2 H 0.119 4
NE M1 -0.333 5
HE HN 0.383 5
CZ A6 0.000 6
NH1 M1 -0.333 7
HH1 HN 0.333 7
NH2 M2 -0.666 8
HH21 HN 0.333 8
HH22 HN 0.333 8
C Aprime 0.380 9
O O -0.380 9
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB CG
CG HG1
CG HG2
CG CD
CD HD1
CD HD2
CD NE
NE HE
NE CZ
CZ NH1
CZ NH2
NH1 HH1
NH2 HH21
NH2 HH22
C O
-C N
[ dihedrals ]
-CA -C N CA
-C N CA C
N CA CB CG
N CA C +N
CA CB CG CD
CB CG CD NE
CG CD NE CZ
CD NE CZ NH2
NE CZ NH1 HH1
NE CZ NH2 HH22
[ impropers ]
-C CA N H improper_X_X_N_X
N C CA HA improper_X_X_C_X
N C CA CB improper_N_A_C1_C
CA +N C O improper_X_X_A_X
CA CG CB HB1 improper_X_X_C_X
CA CG CB HB2 improper_X_X_C_X
CB CD CG HG1 improper_X_X_C_X
CB CD CG HG2 improper_X_X_C_X
CG NE CD HD1 improper_X_X_C_X
CG NE CD HD2 improper_X_X_C_X
CD CZ NE HE improper_X_X_M_X
NE NH1 CZ NH2 improper_X_X_A_X
CZ HH21 NH2 HH22 improper_X_X_M_X
[ ASN ]
[ atoms ]
N N1 -0.333 0
H HN 0.333 0
CA C1 -0.119 1
HA H 0.119 1
CB C2 -0.238 2
HB1 H 0.119 2
HB2 H 0.119 2
CG Aprime 0.380 3
OD1 O -0.380 3
ND2 N2 -0.666 4
HD21 HN 0.333 4
HD22 HN 0.333 4
C Aprime 0.380 5
O O -0.380 5
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB CG
CG OD1
CG ND2
ND2 HD21
ND2 HD22
C O
-C N
[ dihedrals ]
-CA -C N CA
-C N CA C
N CA CB CG
N CA C +N
CA CB CG ND2
CB CG ND2 HD22
[ impropers ]
-C CA N H improper_X_X_N_X
N C CA HA improper_X_X_C_X
N C CA CB improper_N_A_C1_C
CA +N C O improper_X_X_A_X
CA CG CB HB1 improper_X_X_C_X
CA CG CB HB2 improper_X_X_C_X
CB ND2 CG OD1 improper_X_X_A_X
CG HD22 ND2 HD21 improper_X_X_N_X
[ ASP ]
[ atoms ]
N N1 -0.333 0
H HN 0.333 0
CA C1 -0.119 1
HA H 0.119 1
CB C2 -0.238 2
HB1 H 0.119 2
HB2 H 0.119 2
CG Abis 0.640 3
OD1 Obis -0.420 3
OD2 Obis -0.420 3
C Aprime 0.380 4
O O -0.380 4
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB CG
CG OD1
CG OD2
C O
-C N
[ dihedrals ]
-CA -C N CA
-C N CA C
N CA CB CG
N CA C +N
CA CB CG OD2
[ impropers ]
-C CA N H improper_X_X_N_X
N C CA HA improper_X_X_C_X
N C CA CB improper_N_A_C1_C
CA +N C O improper_X_X_A_X
CA CG CB HB1 improper_X_X_C_X
CA CG CB HB2 improper_X_X_C_X
CB OD2 CG OD1 improper_X_X_A_X
[ ASPH ]
[ atoms ]
N N1 -0.333 0
H HN 0.333 0
CA C1 -0.119 1
HA H 0.119 1
CB C2 -0.238 2
HB1 H 0.119 2
HB2 H 0.119 2
CG Aprime 0.380 3
OD1 O -0.380 3
OD2 OH -0.433 4
HD2 HO 0.433 4
C Aprime 0.380 5
O O -0.380 5
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB CG
CG OD1
CG OD2
OD2 HD2
C O
-C N
[ dihedrals ]
-CA -C N CA
-C N CA C
N CA CB CG
N CA C +N
CA CB CG OD2
CB CG OD2 HD2
[ impropers ]
-C CA N H improper_X_X_N_X
N C CA HA improper_X_X_C_X
N C CA CB improper_N_A_C1_C
CA +N C O improper_X_X_A_X
CA CG CB HB1 improper_X_X_C_X
CA CG CB HB2 improper_X_X_C_X
OD2 CB CG OD1 improper_X_X_A_X
[ CYS2 ] ; aka CYX
[ atoms ]
N N1 -0.333 0
H HN 0.333 0
CA C1 -0.119 1
HA H 0.119 1
CB C2 -0.238 2
HB1 H 0.119 2
HB2 H 0.119 2
SG S 0.000 3
C Aprime 0.380 4
O O -0.380 4
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB SG
C O
-C N
[ dihedrals ]
-CA -C N CA
-C N CA C
N CA CB SG
N CA C +N
[ impropers ]
-C CA N H improper_X_X_N_X
N C CA HA improper_X_X_C_X
N C CA CB improper_N_A_C1_C
CA +N C O improper_X_X_A_X
CA SG CB HB1 improper_X_X_C_X
CA SG CB HB2 improper_X_X_C_X
[ CYSH ]
[ atoms ]
N N1 -0.333 0
H HN 0.333 0
CA C1 -0.119 1
HA H 0.119 1
CB C2 -0.238 2
HB1 H 0.119 2
HB2 H 0.119 2
SG SH -0.200 3
HG H 0.200 3
C Aprime 0.380 4
O O -0.380 4
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB SG
SG HG
C O
-C N
[ dihedrals ]
-CA -C N CA
-C N CA C
N CA CB SG
CA CB SG HG
N CA C +N
[ impropers ]
-C CA N H improper_X_X_N_X
N C CA HA improper_X_X_C_X
N C CA CB improper_N_A_C1_C
CA +N C O improper_X_X_A_X
CA SG CB HB1 improper_X_X_C_X
CA SG CB HB2 improper_X_X_C_X
[ CYH ] ; same as cysh
[ atoms ]
N N1 -0.333 0
H HN 0.333 0
CA C1 -0.119 1
HA H 0.119 1
CB C2 -0.238 2
HB1 H 0.119 2
HB2 H 0.119 2
SG SH -0.200 3
HG H 0.200 3
C Aprime 0.380 4
O O -0.380 4
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB SG
SG HG
C O
-C N
[ dihedrals ]
-CA -C N CA
-C N CA C
N CA CB SG
CA CB SG HG
N CA C +N
[ impropers ]
-C CA N H improper_X_X_N_X
N C CA HA improper_X_X_C_X
N C CA CB improper_N_A_C1_C
CA +N C O improper_X_X_A_X
CA SG CB HB1 improper_X_X_C_X
CA SG CB HB2 improper_X_X_C_X
[ GLN ]
[ atoms ]
N N1 -0.333 0
H HN 0.333 0
CA C1 -0.119 1
HA H 0.119 1
CB C2 -0.238 2
HB1 H 0.119 2
HB2 H 0.119 2
CG C2 -0.238 3
HG1 H 0.119 3
HG2 H 0.119 3
CD Aprime 0.380 4
OE1 O -0.380 4
NE2 N2 -0.666 5
HE21 HN 0.333 5
HE22 HN 0.333 5
C Aprime 0.380 6
O O -0.380 6
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB CG
CG HG1
CG HG2
CG CD
CD OE1
CD NE2
NE2 HE21
NE2 HE22
C O
-C N
[ dihedrals ]
-CA -C N CA
-C N CA C
N CA CB CG
CA CB CG CD
CB CG CD NE2
CG CD NE2 HE22
N CA C +N
[ impropers ]
-C CA N H improper_X_X_N_X
N C CA HA improper_X_X_C_X
N C CA CB improper_N_A_C1_C
CA +N C O improper_X_X_A_X
CA CG CB HB1 improper_X_X_C_X
CA CG CB HB2 improper_X_X_C_X
CB CD CG HG1 improper_X_X_C_X
CB CD CG HG2 improper_X_X_C_X
CG NE2 CD OE1 improper_X_X_A_X
CD HE22 NE2 HE21 improper_X_X_N_X
[ GLU ]
[ atoms ]
N N1 -0.333 0
H HN 0.333 0
CA C1 -0.119 1
HA H 0.119 1
CB C2 -0.238 2
HB1 H 0.119 2
HB2 H 0.119 2
CG C2 -0.238 3
HG1 H 0.119 3
HG2 H 0.119 3
CD Abis 0.640 4
OE1 Obis -0.420 4
OE2 Obis -0.420 4
C Aprime 0.380 5
O O -0.380 5
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB CG
CG HG1
CG HG2
CG CD
CD OE1
CD OE2
C O
-C N
[ dihedrals ]
-CA -C N CA
-C N CA C
N CA CB CG
N CA C +N
CA CB CG CD
CB CG CD OE2
[ impropers ]
-C CA N H improper_X_X_N_X
N C CA HA improper_X_X_C_X
N C CA CB improper_N_A_C1_C
CA CG CB HB1 improper_X_X_C_X
CA CG CB HB2 improper_X_X_C_X
CA +N C O improper_X_X_A_X
CB CD CG HG1 improper_X_X_C_X
CB CD CG HG2 improper_X_X_C_X
CG OE2 CD OE1 improper_X_X_A_X
[ GLUH ]
[ atoms ]
N N1 -0.333 1
H HN 0.333 1
CA C1 -0.119 1
HA H 0.119 1
CB C2 -0.238 2
HB1 H 0.119 2
HB2 H 0.119 2
CG C2 -0.238 3
HG1 H 0.119 3
HG2 H 0.119 3
CD Aprime 0.380 4
OE1 O -0.380 4
OE2 OH -0.433 5
HE2 HO 0.433 5
C Aprime 0.380 6
O O -0.380 6
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB CG
CG HG1
CG HG2
CG CD
CD OE1
CD OE2
OE2 HE2
C O
-C N
[ dihedrals ]
-CA -C N CA
-C N CA C
N CA CB CG
N CA C +N
CA CB CG CD
CB CG CD OE2
CG CD OE2 HE2
[ impropers ]
-C CA N H improper_X_X_N_X
N C CA HA improper_X_X_C_X
N C CA CB improper_N_A_C1_C
CA CG CB HB1 improper_X_X_C_X
CA CG CB HB2 improper_X_X_C_X
CB CD CG HG1 improper_X_X_C_X
CB CD CG HG2 improper_X_X_C_X
CG OE2 CD OE1 improper_X_X_A_X
CA +N C O improper_X_X_A_X
[ GLY ]
[ atoms ]
N N1 -0.333 0
H HN 0.333 0
CA C2 -0.238 1
HA1 H 0.119 1
HA2 H 0.119 1
C Aprime 0.380 2
O O -0.380 2
[ bonds ]
N H
N CA
CA HA1
CA HA2
CA C
C O
-C N
[ dihedrals ]
-CA -C N CA
-C N CA C
N CA C +N
[ impropers ]
-C CA N H improper_X_X_N_X
N C CA HA1 improper_X_X_C_X
N C CA HA2 improper_X_X_C_X
CA +N C O improper_X_X_A_X
[ HISA ] ; A.K.A. HISD/HID
[ atoms ]
N N1 -0.333 0
H HN 0.333 0
CA C1 -0.119 1
HA H 0.119 1
CB C2 -0.238 2
HB1 H 0.119 2
HB2 H 0.119 2
CG A5 0.000 3
ND1 N1 -0.333 4
HD1 HN 0.333 4
CE1 A5 0.081 5
HE1 H 0.119 5
NE2 L5 -0.400 5
CD2 A5 0.081 5
HD2 H 0.119 5
C Aprime 0.380 6
O O -0.380 6
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB CG
CG ND1
CG CD2
ND1 HD1
ND1 CE1
CD2 HD2
CD2 NE2
CE1 HE1
CE1 NE2
C O
-C N
[ dihedrals ]
-CA -C N CA
-C N CA C
N CA CB CG
N CA C +N
CA CB CG CD2
CB CG ND1 CE1
CG ND1 CE1 NE2
ND1 CE1 NE2 CD2
CE1 NE2 CD2 CG
[ impropers ]
-C CA N H improper_X_X_N_X
N C CA HA improper_X_X_C_X
N C CA CB improper_N_A_C1_C
CA CG CB HB1 improper_X_X_C_X
CA CG CB HB2 improper_X_X_C_X
CB CD2 CG ND1 improper_X_X_A_X
CG CE1 ND1 HD1 improper_X_X_N_X
ND1 NE2 CE1 HE1 improper_X_X_A_X
NE2 CG CD2 HD2 improper_X_X_A_X
CA +N C O improper_X_X_A_X
[ HID ] ; same as HISA
[ atoms ]
N N1 -0.333 0
H HN 0.333 0
CA C1 -0.119 1
HA H 0.119 1
CB C2 -0.238 2
HB1 H 0.119 2
HB2 H 0.119 2
CG A5 0.000 3
ND1 N1 -0.333 4
HD1 HN 0.333 4
CE1 A5 0.081 5
HE1 H 0.119 5
NE2 L5 -0.400 5
CD2 A5 0.081 5
HD2 H 0.119 5
C Aprime 0.380 6
O O -0.380 6
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB CG
CG ND1
CG CD2
ND1 HD1
ND1 CE1
CD2 HD2
CD2 NE2
CE1 HE1
CE1 NE2
C O
-C N
[ dihedrals ]
-CA -C N CA
-C N CA C
N CA CB CG
N CA C +N
CA CB CG CD2
CB CG ND1 CE1
CG ND1 CE1 NE2
ND1 CE1 NE2 CD2
CE1 NE2 CD2 CG
[ impropers ]
-C CA N H improper_X_X_N_X
N C CA HA improper_X_X_C_X
N C CA CB improper_N_A_C1_C
CA CG CB HB1 improper_X_X_C_X
CA CG CB HB2 improper_X_X_C_X
CB CD2 CG ND1 improper_X_X_A_X
CG CE1 ND1 HD1 improper_X_X_N_X
ND1 NE2 CE1 HE1 improper_X_X_A_X
NE2 CG CD2 HD2 improper_X_X_A_X
CA +N C O improper_X_X_A_X
[ HIS1 ] Identical to HISA
[ atoms ]
N N1 -0.333 0
H HN 0.333 0
CA C1 -0.119 1
HA H 0.119 1
CB C2 -0.238 2
HB1 H 0.119 2
HB2 H 0.119 2
CG A5 0.000 3
ND1 N1 -0.333 4
HD1 HN 0.333 4
CE1 A5 0.081 5
HE1 H 0.119 5
NE2 L5 -0.400 5
CD2 A5 0.081 5
HD2 H 0.119 5
C Aprime 0.380 6
O O -0.380 6
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB CG
CG ND1
CG CD2
ND1 HD1
ND1 CE1
CD2 HD2
CD2 NE2
CE1 HE1
CE1 NE2
C O
-C N
[ dihedrals ]
-CA -C N CA
-C N CA C
N CA CB CG
N CA C +N
CA CB CG CD2
CB CG ND1 CE1
CG ND1 CE1 NE2
ND1 CE1 NE2 CD2
CE1 NE2 CD2 CG
[ impropers ]
-C CA N H improper_X_X_N_X
N C CA HA improper_X_X_C_X
N C CA CB improper_N_A_C1_C
CA CG CB HB1 improper_X_X_C_X
CA CG CB HB2 improper_X_X_C_X
CB CD2 CG ND1 improper_X_X_A_X
CG CE1 ND1 HD1 improper_X_X_N_X
ND1 NE2 CE1 HE1 improper_X_X_A_X
NE2 CG CD2 HD2 improper_X_X_A_X
CA +N C O improper_X_X_A_X
[ HISB ] ; A.K.A. HISE/HIE
[ atoms ]
N N1 -0.333 0
H HN 0.333 0
CA C1 -0.119 1
HA H 0.119 1
CB C2 -0.238 2
HB1 H 0.119 2
HB2 H 0.119 2
CG A5 0.200 3
ND1 L5 -0.400 3
CE1 A5 0.081 3
HE1 H 0.119 3
NE2 N1 -0.333 4
HE2 HN 0.333 4
CD2 A5 -0.119 5
HD2 H 0.119 5
C Aprime 0.380 6
O O -0.380 6
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB CG
CG ND1
CG CD2
ND1 CE1
CD2 HD2
CD2 NE2
CE1 HE1
CE1 NE2
NE2 HE2
C O
-C N
[ dihedrals ]
-CA -C N CA
-C N CA C
N CA CB CG
N CA C +N
CA CB CG CD2
CB CG ND1 CE1
CG ND1 CE1 NE2
ND1 CE1 NE2 CD2
CE1 NE2 CD2 CG
[ impropers ]
-C CA N H improper_X_X_N_X
N C CA HA improper_X_X_C_X
N C CA CB improper_N_A_C1_C
CA CG CB HB1 improper_X_X_C_X
CA CG CB HB2 improper_X_X_C_X
CB CD2 CG ND1 improper_X_X_A_X
ND1 NE2 CE1 HE1 improper_X_X_A_X
CE1 CD2 NE2 HE2 improper_X_X_N_X
NE2 CG CD2 HD2 improper_X_X_A_X
CA +N C O improper_X_X_A_X
[ HIE ] ; same as HISB
[ atoms ]
N N1 -0.333 0
H HN 0.333 0
CA C1 -0.119 1
HA H 0.119 1
CB C2 -0.238 2
HB1 H 0.119 2
HB2 H 0.119 2
CG A5 0.200 3
ND1 L5 -0.400 3
CE1 A5 0.081 3
HE1 H 0.119 3
NE2 N1 -0.333 4
HE2 HN 0.333 4
CD2 A5 -0.119 5
HD2 H 0.119 5
C Aprime 0.380 6
O O -0.380 6
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB CG
CG ND1
CG CD2
ND1 CE1
CD2 HD2
CD2 NE2
CE1 HE1
CE1 NE2
NE2 HE2
C O
-C N
[ dihedrals ]
-CA -C N CA
-C N CA C
N CA CB CG
N CA C +N
CA CB CG CD2
CB CG ND1 CE1
CG ND1 CE1 NE2
ND1 CE1 NE2 CD2
CE1 NE2 CD2 CG
[ impropers ]
-C CA N H improper_X_X_N_X
N C CA HA improper_X_X_C_X
N C CA CB improper_N_A_C1_C
CA CG CB HB1 improper_X_X_C_X
CA CG CB HB2 improper_X_X_C_X
CB CD2 CG ND1 improper_X_X_A_X
ND1 NE2 CE1 HE1 improper_X_X_A_X
CE1 CD2 NE2 HE2 improper_X_X_N_X
NE2 CG CD2 HD2 improper_X_X_A_X
CA +N C O improper_X_X_A_X
[ HISH ] ; also known as HISP (or HIS+)
[ atoms ]
N N1 -0.333 1
H HN 0.333 1
CA C1 -0.119 1
HA H 0.119 1
CB C2 -0.238 2
HB1 H 0.119 2
HB2 H 0.119 2
CG A5 0.000 3
ND1 N1 -0.300 4
HD1 HN 0.375 4
CE1 A5 -0.119 6
HE1 H 0.119 6
NE2 N1 -0.300 7
HE2 HN 0.375 7
CD2 A5 -0.119 5
HD2 H 0.119 5
C Aprime 0.380 8
O O -0.380 8
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB CG
CG ND1
CG CD2
ND1 HD1
ND1 CE1
CD2 HD2
CD2 NE2
CE1 HE1
CE1 NE2
NE2 HE2
C O
-C N
[ dihedrals ]
-CA -C N CA
-C N CA C
N CA CB CG
N CA C +N
CA CB CG CD2
CB CG ND1 CE1
CG ND1 CE1 NE2
ND1 CE1 NE2 CD2
CE1 NE2 CD2 CG
[ impropers ]
-C CA N H improper_X_X_N_X
N C CA HA improper_X_X_C_X
N C CA CB improper_N_A_C1_C
CA CG CB HB1 improper_X_X_C_X
CA CG CB HB2 improper_X_X_C_X
CB CD2 CG ND1 improper_X_X_A_X
CG CE1 ND1 HD1 improper_X_X_N_X
ND1 NE2 CE1 HE1 improper_X_X_A_X
CE1 CD2 NE2 HE2 improper_X_X_N_X
NE2 CG CD2 HD2 improper_X_X_A_X
CA +N C O improper_X_X_A_X
[ HIP ] ; same as HISH
[ atoms ]
N N1 -0.333 1
H HN 0.333 1
CA C1 -0.119 1
HA H 0.119 1
CB C2 -0.238 2
HB1 H 0.119 2
HB2 H 0.119 2
CG A5 0.000 3
ND1 N1 -0.300 4
HD1 HN 0.375 4
CE1 A5 -0.119 6
HE1 H 0.119 6
NE2 N1 -0.300 7
HE2 HN 0.375 7
CD2 A5 -0.119 5
HD2 H 0.119 5
C Aprime 0.380 8
O O -0.380 8
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB CG
CG ND1
CG CD2
ND1 HD1
ND1 CE1
CD2 HD2
CD2 NE2
CE1 HE1
CE1 NE2
NE2 HE2
C O
-C N
[ dihedrals ]
-CA -C N CA
-C N CA C
N CA CB CG
N CA C +N
CA CB CG CD2
CB CG ND1 CE1
CG ND1 CE1 NE2
ND1 CE1 NE2 CD2
CE1 NE2 CD2 CG
[ impropers ]
-C CA N H improper_X_X_N_X
N C CA HA improper_X_X_C_X
N C CA CB improper_N_A_C1_C
CA CG CB HB1 improper_X_X_C_X
CA CG CB HB2 improper_X_X_C_X
CB CD2 CG ND1 improper_X_X_A_X
CG CE1 ND1 HD1 improper_X_X_N_X
ND1 NE2 CE1 HE1 improper_X_X_A_X
CE1 CD2 NE2 HE2 improper_X_X_N_X
NE2 CG CD2 HD2 improper_X_X_A_X
CA +N C O improper_X_X_A_X
[ HOH ]
; SPC and encad water have identical charges.
; Include encadwater.itp instead of spc.itp to use the flexible encad bonds/angles
; instead of the rigid SPC model.
[ atoms ]
OW OW -0.82 0
HW1 HW 0.41 0
HW2 HW 0.41 0
[ bonds ]
OW HW1
OW HW2
[ ILE ]
[ atoms ]
N N1 -0.333 0
H HN 0.333 0
CA C1 -0.119 1
HA H 0.119 1
CB C1 -0.119 2
HB H 0.119 2
CG2 C3 -0.357 3
HG21 H 0.119 3
HG22 H 0.119 3
HG23 H 0.119 3
CG1 C2 -0.238 4
HG11 H 0.119 4
HG12 H 0.119 4
CD C3 -0.357 5
HD1 H 0.119 5
HD2 H 0.119 5
HD3 H 0.119 5
C Aprime 0.380 6
O O -0.380 6
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB
CB CG1
CB CG2
CG1 HG11
CG1 HG12
CG1 CD
CG2 HG21
CG2 HG22
CG2 HG23
CD HD1
CD HD2
CD HD3
C O
-C N
[ dihedrals ]
-CA -C N CA
-C N CA C
N CA CB CG1
N CA C +N
CA CB CG2 HG23
CA CB CG1 CD
CB CG1 CD HD3
[ impropers ]
-C CA N H improper_X_X_N_X
N C CA HA improper_X_X_C_X
N C CA CB improper_N_A_C1_C
CA CG1 CB CG2 improper_C1_C2_C1_C3
CA CG1 CB HB improper_X_X_C_X
CB CD CG1 HG11 improper_X_X_C_X
CB CD CG1 HG12 improper_X_X_C_X
CG1 HD3 CD HD1 improper_X_X_C_X
CG1 HD3 CD HD2 improper_X_X_C_X
CB HG23 CG2 HG21 improper_X_X_C_X
CB HG23 CG2 HG22 improper_X_X_C_X
CA +N C O improper_X_X_A_X
[ LEU ]
[ atoms ]
N N1 -0.333 0
H HN 0.333 0
CA C1 -0.119 1
HA H 0.119 1
CB C2 -0.238 2
HB1 H 0.119 2
HB2 H 0.119 2
CG C1 -0.119 3
HG H 0.119 3
CD1 C3 -0.357 4
HD11 H 0.119 4
HD12 H 0.119 4
HD13 H 0.119 4
CD2 C3 -0.357 5
HD21 H 0.119 5
HD22 H 0.119 5
HD23 H 0.119 5
C Aprime 0.380 6
O O -0.380 6
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB CG
CG HG
CG CD1
CG CD2
CD1 HD11
CD1 HD12
CD1 HD13
CD2 HD21
CD2 HD22
CD2 HD23
C O
-C N
[ dihedrals ]
-CA -C N CA
-C N CA C
N CA CB CG
N CA C +N
CA CB CG CD2
CB CG CD1 HD13
CB CG CD2 HD23
[ impropers ]
-C CA N H improper_X_X_N_X
N C CA HA improper_X_X_C_X
N C CA CB improper_N_A_C1_C
CA CG CB HB1 improper_X_X_C_X
CA CG CB HB2 improper_X_X_C_X
CB CD2 CG HG improper_X_X_C_X
CB CD2 CG CD1 improper_X_X_C_X
CG HD13 CD1 HD11 improper_X_X_C_X
CG HD13 CD1 HD12 improper_X_X_C_X
CG HD23 CD2 HD21 improper_X_X_C_X
CG HD23 CD2 HD22 improper_X_X_C_X
CA +N C O improper_X_X_A_X
[ LYS ] ; non-protonated - see LYSH for the most common state.
[ atoms ]
N N1 -0.333 0
H HN 0.333 0
CA C1 -0.119 1
HA H 0.119 1
CB C2 -0.238 2
HB1 H 0.119 2
HB2 H 0.119 2
CG C2 -0.238 3
HG1 H 0.119 3
HG2 H 0.119 3
CD C2 -0.238 4
HD1 H 0.119 4
HD2 H 0.119 4
CE C2 -0.238 5
HE1 H 0.119 5
HE2 H 0.119 5
NZ N2 -0.666 6
HZ1 HN 0.333 6
HZ2 HN 0.333 6
C Aprime 0.380 7
O O -0.380 7
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB CG
CG HG1
CG HG2
CG CD
CD HD1
CD HD2
CD CE
CE HE1
CE HE2
CE NZ
NZ HZ1
NZ HZ2
C O
-C N
[ dihedrals ]
-CA -C N CA
-C N CA C
N CA CB CG
N CA C +N
CA CB CG CD
CB CG CD CE
CG CD CE NZ
CD CE NZ HZ2
[ impropers ]
-C CA N H improper_X_X_N_X
N C CA HA improper_X_X_C_X
N C CA CB improper_N_A_C1_C
CA CG CB HB1 improper_X_X_C_X
CA CG CB HB2 improper_X_X_C_X
CB CD CG HG1 improper_X_X_C_X
CB CD CG HG2 improper_X_X_C_X
CG CE CD HD1 improper_X_X_C_X
CG CE CD HD2 improper_X_X_C_X
CD NZ CE HE1 improper_X_X_C_X
CD NZ CE HE2 improper_X_X_C_X
CE HZ2 NZ HZ1 improper_X_X_M_X
CA +N C O improper_X_X_A_X
[ LYSH ]
[ atoms ]
N N1 -0.333 0
H HN 0.333 0
CA C1 -0.119 1
HA H 0.119 1
CB C2 -0.238 2
HB1 H 0.119 2
HB2 H 0.119 2
CG C2 -0.238 3
HG1 H 0.119 3
HG2 H 0.119 3
CD C2 -0.238 4
HD1 H 0.119 4
HD2 H 0.119 4
CE C2 -0.238 5
HE1 H 0.119 5
HE2 H 0.119 5
NZ M3 -0.910 6
HZ1 HN 0.370 6
HZ2 HN 0.370 6
HZ3 HN 0.370 6
C Aprime 0.380 7
O O -0.380 7
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB CG
CG HG1
CG HG2
CG CD
CD HD1
CD HD2
CD CE
CE HE1
CE HE2
CE NZ
NZ HZ1
NZ HZ2
NZ HZ3
C O
-C N
[ dihedrals ]
-CA -C N CA
-C N CA C
N CA CB CG
N CA C +N
CA CB CG CD
CB CG CD CE
CG CD CE NZ
CD CE NZ HZ3
[ impropers ]
-C CA N H improper_X_X_N_X
N C CA HA improper_X_X_C_X
N C CA CB improper_N_A_C1_C
CA CG CB HB1 improper_X_X_C_X
CA CG CB HB2 improper_X_X_C_X
CB CD CG HG1 improper_X_X_C_X
CB CD CG HG2 improper_X_X_C_X
CG CE CD HD1 improper_X_X_C_X
CG CE CD HD2 improper_X_X_C_X
CD NZ CE HE1 improper_X_X_C_X
CD NZ CE HE2 improper_X_X_C_X
CE HZ3 NZ HZ1 improper_X_X_M3_X
CE HZ3 NZ HZ2 improper_X_X_M3_X
CA +N C O improper_X_X_A_X
[ MET ]
[ atoms ]
N N1 -0.333 0
H HN 0.333 0
CA C1 -0.119 1
HA H 0.119 1
CB C2 -0.238 2
HB1 H 0.119 2
HB2 H 0.119 2
CG C2 -0.238 3
HG1 H 0.119 3
HG2 H 0.119 3
SD S 0.000 4
CE C3 -0.357 5
HE1 H 0.119 5
HE2 H 0.119 5
HE3 H 0.119 5
C Aprime 0.380 6
O O -0.380 6
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB CG
CG HG1
CG HG2
CG SD
SD CE
CE HE1
CE HE2
CE HE3
C O
-C N
[ dihedrals ]
-CA -C N CA
-C N CA C
N CA CB CG
N CA C +N
CA CB CG SD
CB CG SD CE
CG SD CE HE3
[ impropers ]
-C CA N H improper_X_X_N_X
N C CA HA improper_X_X_C_X
N C CA CB improper_N_A_C1_C
CA CG CB HB1 improper_X_X_C_X
CA CG CB HB2 improper_X_X_C_X
CB SD CG HG1 improper_X_X_C_X
CB SD CG HG2 improper_X_X_C_X
SD HE3 CE HE1 improper_X_X_C_X
SD HE3 CE HE2 improper_X_X_C_X
CA +N C O improper_X_X_A_X
[ NAC ] ; metylamide, a.k.a NMA.
[ atoms ]
N N1 -0.333 1
H HN 0.333 1
CH3 C3 -0.357 2
HH31 H 0.119 2
HH32 H 0.119 2
HH33 H 0.119 2
[ bonds ]
N H
N CH3
CH3 HH31
CH3 HH32
CH3 HH33
-C N
[ dihedrals ]
-CA -C N CH3
-C N CH3 HH33
[ impropers ]
-C CH3 N H improper_X_X_N_X
N HH33 CH3 HH31 improper_X_X_C_X
N HH33 CH3 HH32 improper_X_X_C_X
[ NH2 ]
[ atoms ]
N N2 -0.666 1
H1 HN 0.333 1
H2 HN 0.333 1
[ bonds ]
-C N
N H1
N H2
[ dihedrals ]
-CA -C N H2
[ impropers ]
-C H2 N H1 improper_X_X_N_X
[ NHE ]
; same as NH2
[ atoms ]
N N2 -0.666 1
H1 HN 0.333 1
H2 HN 0.333 1
[ bonds ]
-C N
N H1
N H2
[ dihedrals ]
-CA -C N H2
[ impropers ]
-C H2 N H1 improper_X_X_N_X
[ PHE ]
[ atoms ]
N N1 -0.333 0
H HN 0.333 0
CA C1 -0.119 1
HA H 0.119 1
CB C2 -0.238 2
HB1 H 0.119 2
HB2 H 0.119 2
CG A6 0.000 3
CD1 A6 -0.119 4
HD1 H 0.119 4
CE1 A6 -0.119 5
HE1 H 0.119 5
CZ A6 -0.119 6
HZ H 0.119 6
CE2 A6 -0.119 7
HE2 H 0.119 7
CD2 A6 -0.119 8
HD2 H 0.119 8
C Aprime 0.380 9
O O -0.380 9
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB CG
CG CD1
CG CD2
CD1 HD1
CD1 CE1
CD2 HD2
CD2 CE2
CE1 HE1
CE1 CZ
CE2 HE2
CE2 CZ
CZ HZ
C O
-C N
[ dihedrals ]
-CA -C N CA
-C N CA C
N CA CB CG
N CA C +N
CA CB CG CD2
CB CG CD1 CE1
CB CG CD2 CE2
CG CD1 CE1 CZ
CD1 CE1 CZ CE2
CE1 CZ CE2 CD2
CZ CE2 CD2 CG
[ impropers ]
-C CA N H improper_X_X_N_X
N C CA HA improper_X_X_C_X
N C CA CB improper_N_A_C1_C
CA CG CB HB1 improper_X_X_C_X
CA CG CB HB2 improper_X_X_C_X
CB CD2 CG CD1 improper_X_X_A_X
CG CE1 CD1 HD1 improper_X_X_A_X
CD1 CZ CE1 HE1 improper_X_X_A_X
CE1 CE2 CZ HZ improper_X_X_A_X
CE2 CG CD2 HD2 improper_X_X_A_X
CZ CD2 CE2 HE2 improper_X_X_A_X
CA +N C O improper_X_X_A_X
[ PRO ]
[ atoms ]
N N 0.000 0
CA C1 -0.119 1
HA H 0.119 1
CB CP -0.238 2
HB1 H 0.119 2
HB2 H 0.119 2
CG CP -0.238 3
HG1 H 0.119 3
HG2 H 0.119 3
CD CP -0.238 4
HD1 H 0.119 4
HD2 H 0.119 4
C Aprime 0.380 5
O O -0.380 5
[ bonds ]
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB CG
CG HG1
CG HG2
CG CD
CD HD1
CD HD2
CD N
C O
-C N
[ dihedrals ]
-CA -C N CD
-C N CA C
N CA CB CG
N CA C +N
CA CB CG CD
CB CG CD N
[ impropers ]
-C CA N H improper_X_X_N_X
N C CA HA improper_X_X_C_X
N C CA CB improper_N_A_C1_C
CA CG CB HB1 improper_X_X_C_X
CA CG CB HB2 improper_X_X_C_X
CB CD CG HG1 improper_X_X_C_X
CB CD CG HG2 improper_X_X_C_X
CG N CD HD1 improper_X_X_C_X
CG N CD HD2 improper_X_X_C_X
-C CD N CA improper_X_X_N_X
CA +N C O improper_X_X_A_X
[ SER ]
[ atoms ]
N N1 -0.333 0
H HN 0.333 0
CA C1 -0.119 1
HA H 0.119 1
CB C2 -0.238 2
HB1 H 0.119 2
HB2 H 0.119 2
OG OH -0.433 3
HG HO 0.433 3
C Aprime 0.380 4
O O -0.380 4
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB OG
OG HG
C O
-C N
[ dihedrals ]
-CA -C N CA
-C N CA C
N CA CB OG
N CA C +N
CA CB OG HG
[ impropers ]
-C CA N H improper_X_X_N_X
N C CA HA improper_X_X_C_X
N C CA CB improper_N_A_C1_C
CA OG CB HB1 improper_X_X_C_X
CA OG CB HB2 improper_X_X_C_X
CA +N C O improper_X_X_A_X
[ THR ]
[ atoms ]
N N1 -0.333 0
H HN 0.333 0
CA C1 -0.119 1
HA H 0.119 1
CB C1 -0.119 2
HB H 0.119 2
OG1 OH -0.433 3
HG1 HO 0.433 3
CG2 C3 -0.357 4
HG21 H 0.119 4
HG22 H 0.119 4
HG23 H 0.119 4
C Aprime 0.380 5
O O -0.380 5
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB
CB OG1
CB CG2
OG1 HG1
CG2 HG21
CG2 HG22
CG2 HG23
C O
-C N
[ dihedrals ]
-CA -C N CA
-C N CA C
N CA CB CG2
N CA C +N
CA CB OG1 HG1
CA CB CG2 HG23
[ impropers ]
-C CA N H improper_X_X_N_X
N C CA HA improper_X_X_C_X
N C CA CB improper_N_A_C1_C
CA CG2 CB OG1 improper_X_X_C_X
CA CG2 CB HB improper_X_X_C_X
CB HG23 CG2 HG21 improper_X_X_C_X
CB HG23 CG2 HG22 improper_X_X_C_X
CA +N C O improper_X_X_A_X
[ TRP ]
[ atoms ]
N N1 -0.333 0
H HN 0.333 0
CA C1 -0.119 1
HA H 0.119 1
CB C2 -0.238 2
HB1 H 0.119 2
HB2 H 0.119 2
CG A5 0.000 3
CD1 A5 -0.119 4
HD1 H 0.119 4
NE1 N1 -0.333 5
HE1 HN 0.333 5
CE2 A7 0.000 6
CZ2 A6 -0.119 7
HZ2 H 0.119 7
CH2 A6 -0.119 8
HH2 H 0.119 8
CZ3 A6 -0.119 9
HZ3 H 0.119 9
CE3 A6 -0.119 10
HE3 H 0.119 10
CD2 A7 0.000 11
C Aprime 0.380 12
O O -0.380 12
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB CG
CG CD1
CG CD2
CD1 HD1
CD1 NE1
CD2 CE2
CD2 CE3
NE1 HE1
NE1 CE2
CE2 CZ2
CE3 HE3
CE3 CZ3
CZ2 HZ2
CZ2 CH2
CZ3 HZ3
CZ3 CH2
CH2 HH2
C O
-C N
[ dihedrals ]
-CA -C N CA
-C N CA C
N CA CB CG
N CA C +N
CA CB CG CD2
CB CG CD1 NE1
CG CD1 NE1 CE2
CD1 NE1 CE2 CD2
NE1 CE2 CD2 CE3
NE1 CE2 CZ2 CH2
CE2 CZ2 CH2 CZ3
CZ2 CH2 CZ3 CE3
CH2 CZ3 CE3 CD2
CZ3 CE3 CD2 CE2
CB CG CD2 CE3
[ impropers ]
-C CA N H improper_X_X_N_X
CA +N C O improper_X_X_A_X
N C CA CB improper_N_A_C1_C
N C CA HA improper_X_X_C_X
CA CG CB HB1 improper_X_X_C_X
CA CG CB HB2 improper_X_X_C_X
CB CD2 CG CD1 improper_X_X_A_X
CG NE1 CD1 HD1 improper_X_X_A_X
CD1 CE2 NE1 HE1 improper_X_X_N_X
NE1 CD2 CE2 CZ2 improper_X_X_A_X
CE2 CH2 CZ2 HZ2 improper_X_X_A_X
CZ2 CZ3 CH2 HH2 improper_X_X_A_X
CH2 CE3 CZ3 HZ3 improper_X_X_A_X
CZ3 CD2 CE3 HE3 improper_X_X_A_X
CG CD2 CE2 CE3 improper_X_X_A_X
[ TYR ]
[ atoms ]
N N1 -0.333 0
H HN 0.333 0
CA C1 -0.119 1
HA H 0.119 1
CB C2 -0.238 2
HB1 H 0.119 2
HB2 H 0.119 2
CG A6 0.000 3
CD1 A6 -0.119 4
HD1 H 0.119 4
CE1 A6 -0.119 5
HE1 H 0.119 5
CZ A6 0.000 6
OH OH -0.433 7
HH HO 0.433 7
CE2 A6 -0.119 8
HE2 H 0.119 8
CD2 A6 -0.119 9
HD2 H 0.119 9
C Aprime 0.380 10
O O -0.380 10
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB CG
CG CD1
CG CD2
CD1 HD1
CD1 CE1
CD2 HD2
CD2 CE2
CE1 HE1
CE1 CZ
CE2 HE2
CE2 CZ
CZ OH
OH HH
C O
-C N
[ dihedrals ]
-CA -C N CA
-C N CA C
N CA CB CG
N CA C +N
CA CB CG CD2
CB CG CD1 CE1
CB CG CD2 CE2
CG CD1 CE1 CZ
CD1 CE1 CZ CE2
CE1 CZ OH HO
CE1 CZ CE2 CD2
CZ CE2 CD2 CG
[ impropers ]
-C CA N H improper_X_X_N_X
N C CA HA improper_X_X_C_X
N C CA CB improper_N_A_C1_C
CA CG CB HB1 improper_X_X_C_X
CA CG CB HB2 improper_X_X_C_X
CB CD2 CG CD1 improper_X_X_A_X
CG CE1 CD1 HD1 improper_X_X_A_X
CD1 CZ CE1 HE1 improper_X_X_A_X
CE1 CE2 CZ OH improper_X_X_A_X
CE2 CG CD2 HD2 improper_X_X_A_X
CZ CD2 CE2 HE2 improper_X_X_A_X
CA +N C O improper_X_X_A_X
[ VAL ]
[ atoms ]
N N1 -0.333 0
H HN 0.333 0
CA C1 -0.119 1
HA H 0.119 1
CB C1 -0.119 2
HB H 0.119 2
CG1 C3 -0.357 3
HG11 H 0.119 3
HG12 H 0.119 3
HG13 H 0.119 3
CG2 C3 -0.357 4
HG21 H 0.119 4
HG22 H 0.119 4
HG23 H 0.119 4
C Aprime 0.380 5
O O -0.380 5
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB
CB CG1
CB CG2
CG1 HG11
CG1 HG12
CG1 HG13
CG2 HG21
CG2 HG22
CG2 HG23
C O
-C N
[ dihedrals ]
-CA -C N CA
-C N CA C
N CA CB CG2
N CA C +N
CA CB CG2 HG23
CA CB CG1 HG13
[ impropers ]
-C CA N H improper_X_X_N_X
N C CA HA improper_X_X_C_X
N C CA CB improper_N_A_C1_C
CA CG2 CB HB improper_X_X_C_X
CA CG2 CB CG1 improper_X_X_C_X
CB HG13 CG1 HG11 improper_X_X_C_X
CB HG13 CG1 HG12 improper_X_X_C_X
CB HG23 CG2 HG21 improper_X_X_C_X
CB HG23 CG2 HG22 improper_X_X_C_X
CA +N C O improper_X_X_A_X
[ CL ]
[ atoms ]
CL CL -1.000 0
[ NA ]
[ atoms ]
NA NA 1.000 0
[ FE ]
[ atoms ]
FE FE 2.000 0
[ Ar ]
[ atoms ]
AR AR 0.000 0
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