/usr/share/gromacs/top/gromos53a5.ff/aminoacids.hdb is in gromacs-data 5.0.2-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 | ABU 1
1 1 H N -C CA
ACEH 1
3 4 HA CA C O
AIB 1
1 1 H N -C CA
ALA 1
1 1 H N -C CA
ARG 4
1 1 H N -C CA
1 1 HE NE CD CZ
2 3 HH1 NH1 CZ NE
2 3 HH2 NH2 CZ NE
ARGN 4
1 1 H N -C CA
1 1 HE NE CD CZ
1 2 HH1 NH1 CZ NE
2 3 HH2 NH2 CZ NE
ASN 2
1 1 H N -C CA
2 3 HD2 ND2 CG CB
ASP 1
1 1 H N -C CA
ASP1 2
1 1 H N -C CA
1 2 HD1 OD1 CG CB
ASPH 2
1 1 H N -C CA
1 2 HD2 OD2 CG CB
ATP 4
2 3 AH6 AN6 AC6 AC5
1 2 AH2* AO2* AC2* AC3*
1 2 AH3* AO3* AC3* AC2*
1 2 AH3G AO3G APG AO2G
BEN 7
1 1 H2 C2 C1 C3
1 1 H3 C3 C2 C4
1 1 H4 C4 C3 C5
1 1 H5 C5 C4 C6
1 1 H6 C6 C5 C1
2 3 H1 N1 C7 C1
2 3 H2 N2 C7 C1
CYS2 1
1 1 H N -C CA
CYSH 2
1 1 H N -C CA
1 2 HG SG CB CA
DADE 3
1 1 H2 C2 N1 N3
1 1 H8 C8 N7 N9
2 3 H6 N6 C6 C5
DTHY 2
1 1 H3 N3 C2 C4
1 1 H6 C6 C5 N1
FAD 7
2 3 HN6 AN6 AC6 AC5
1 2 HO2* AO2* AC2* AC1*
1 2 HO3* AO3* AC3* AC2*
1 2 H4* O4* C4* C5*
1 2 H3* O3* C3* C4*
1 2 H2* O2* C2* C3*
1 2 H3 N3 C4 C4A
GLN 2
1 1 H N -C CA
2 3 HE2 NE2 CD CG
GLU 1
1 1 H N -C CA
GLUH 2
1 1 H N -C CA
1 2 HE2 OE2 CD CG
GLY 1
1 1 H N -C CA
HEME 4
1 1 HHA CHA C1A C4D
1 1 HHB CHB C1B C4A
1 1 HHC CHC C1C C4B
1 1 HHD CHD C1D C4C
HIS1 4
1 1 H N -C CA
1 1 HD1 ND1 CG CE1
1 1 HD2 CD2 CG NE2
1 1 HE1 CE1 ND1 NE2
HIS2 4
1 1 H N -C CA
1 1 HD1 ND1 CG CE1
1 1 HD2 CD2 CG NE2
1 1 HE1 CE1 ND1 NE2
HISA 4
1 1 H N -C CA
1 1 HD1 ND1 CG CE1
1 1 HD2 CD2 CG NE2
1 1 HE1 CE1 ND1 NE2
HISB 4
1 1 H N -C CA
1 1 HD2 CD2 CG NE2
1 1 HE1 CE1 ND1 NE2
1 1 HE2 NE2 CE1 CD2
HISH 5
1 1 H N -C CA
1 1 HD1 ND1 CG CE1
1 1 HD2 CD2 CG NE2
1 1 HE1 CE1 ND1 NE2
1 1 HE2 NE2 CE1 CD2
HOH 1
2 7 HW OW
HYP 1
1 2 HD1 OD1 CG CB
ILE 1
1 1 H N -C CA
LEU 1
1 1 H N -C CA
LYS 2
1 1 H N -C CA
2 4 HZ NZ CE CD
LYSH 2
1 1 H N -C CA
3 4 HZ NZ CE CD
MET 1
1 1 H N -C CA
NAC 1
1 1 H N -C CA
NACH 2
1 1 H N -C CA
3 4 HA CA N NH
NH2 1
2 3 H N -C -CA
PHE 6
1 1 H N -C CA
1 1 HD1 CD1 CG CE1
1 1 HD2 CD2 CG CE2
1 1 HE1 CE1 CD1 CZ
1 1 HE2 CE2 CD2 CZ
1 1 HZ CZ CE1 CE2
PHEU 1
1 1 H N -C CA
PHL 7
1 1 H N -C CA
1 1 HD1 CD1 CG CE1
1 1 HD2 CD2 CG CE2
1 1 HE1 CE1 CD1 CZ
1 1 HE2 CE2 CD2 CZ
1 1 HZ CZ CE1 CE2
1 2 HY OY CX CA
SER 2
1 1 H N -C CA
1 2 HG OG CB CA
TFE 1
1 2 H O CH2 C
THR 2
1 1 H N -C CA
1 2 HG1 OG1 CB CA
TRP 7
1 1 H N -C CA
1 1 HD1 CD1 CG NE1
1 1 HE1 NE1 CD1 CE2
1 1 HE3 CE3 CD2 CZ3
1 1 HZ3 CZ3 CE3 CH2
1 1 HH2 CH2 CZ3 CZ2
1 1 HZ2 CZ2 CE2 CH2
TRPU 2
1 1 H N -C CA
1 1 HE1 NE1 CD1 CE2
TYR 6
1 1 H N -C CA
1 1 HD1 CD1 CG CE1
1 1 HD2 CD2 CG CE2
1 1 HE1 CE1 CD1 CZ
1 1 HE2 CE2 CD2 CZ
1 2 HH OH CZ CE1
TYRU 2
1 1 H N -C CA
1 2 HH OH CZ CE1
VAL 1
1 1 H N -C CA
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