/usr/share/gromacs/top/oplsaa.ff/aminoacids.vsd 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 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 | ; If you get a complaint about missing dummy types from pdb2gmx
; is is straightforward to add it here.
; First, determine the bonded atom type (for most forcefields except
; opls it is probably identical to the nonbonded atomtype) for the
; next atom bound to your N or C atom. Check the constrainttypes
; section of the forcefield and determine which type of dummy mass
; is used for an N (or C) bonded to that atomtype.
; In the correct section below you can then add your atomtype
; (not bonded atomtype!), the type of the bound heavy atom, and the
; type of dummy mass to use in this case.
;
; If the dummy is a planar NH2 group you should just write planar
; after the N atomtype name.
; N.B: dummy masses must have names beginning with MNH2* , MNH3* , MCH3*.
[ CH3 ]
opls_135 opls_136 MCH3B
opls_135 opls_137 MCH3B
opls_135 opls_157 MCH3B
opls_135 opls_158 MCH3B
opls_135 opls_224B MCH3B
opls_135 opls_225B MCH3B
opls_135 opls_235 MCH3A
opls_135 opls_283 MCH3B
opls_135 opls_293B MCH3B
opls_135 opls_299 MCH3B
opls_135 opls_912B MCH3B
opls_209 opls_202 MCH3A
[ NH3 ]
opls_287 opls_283 MNH3
opls_287 opls_292 MNH3
opls_287 opls_292B MNH3
opls_287 opls_293 MNH3
opls_287 opls_293B MNH3
opls_287 opls_298 MNH3
opls_287 opls_299 MNH3
[ NH2 ]
opls_237 planar
opls_300 planar
opls_751 planar
opls_900 opls_906 MNH2
opls_900 opls_906B MNH2
opls_900 opls_912B MNH2
; Data for generating dummy aromatic rings.
; Actually we dont need all these bonds and angles,
; but by specifying them here it is easier to improve
; the dummy generation code later.
[ PHE ]
CG CD1 0.140
CG CD2 0.140
CD1 CE1 0.140
CD2 CE2 0.140
CE1 CZ 0.140
CE2 CZ 0.140
CD1 HD1 0.108
CD2 HD2 0.108
CE1 HE1 0.108
CE2 HE2 0.108
CZ HZ 0.108
CG CD1 CE1 120.0
CD1 CE1 CZ 120.0
CE1 CZ CE2 120.0
CZ CE2 CD2 120.0
CE2 CD2 CG 120.0
CD2 CG CD1 120.0
CG CD1 HD1 120.0
CG CD2 HD2 120.0
HD1 CD1 CE1 120.0
CD1 CE1 HE1 120.0
HE1 CE1 CZ 120.0
CE1 CZ HZ 120.0
HZ CZ CE2 120.0
CZ CE2 HE2 120.0
HE2 CE2 CD2 120.0
HD2 CD2 CG 120.0
[ TYR ]
CG CD1 0.140
CG CD2 0.140
CD1 CE1 0.140
CD2 CE2 0.140
CE1 CZ 0.140
CE2 CZ 0.140
CD1 HD1 0.108
CD2 HD2 0.108
CE1 HE1 0.108
CE2 HE2 0.108
CZ OH 0.1364
OH HH 0.0945
CG CD1 CE1 120.0
CD1 CE1 CZ 120.0
CE1 CZ CE2 120.0
CZ CE2 CD2 120.0
CE2 CD2 CG 120.0
CD2 CG CD1 120.0
CG CD1 HD1 120.0
CG CD2 HD2 120.0
HD1 CD1 CE1 120.0
CD1 CE1 HE1 120.0
HE1 CE1 CZ 120.0
CE1 CZ OH 120.0
CZ OH HH 113.0
OH CZ CE2 120.0
CZ CE2 HE2 120.0
HE2 CE2 CD2 120.0
HD2 CD2 CG 120.0
[ TRP ] ; angles from MD sim, corrected to be perfectly planar
CB CG 0.1495
CG CD1 0.1352
CD1 NE1 0.1381
NE1 CE2 0.138
CE2 CD2 0.1419
CD2 CG 0.1459
CE2 CZ2 0.140
CZ2 CH2 0.140
CH2 CZ3 0.140
CZ3 CE3 0.140
CE3 CD2 0.1404
CD1 HD1 0.108
NE1 HE1 0.101
CE3 HE3 0.108
CZ2 HZ2 0.108
CZ3 HZ3 0.108
CH2 HH2 0.108
CB CG CD1 125.6
CB CG CD2 128.7
CG CD1 NE1 109.7
CD1 NE1 CE2 111.7
NE1 CE2 CD2 104.3
CE2 CD2 CG 108.5
CD2 CG CD1 105.7
NE1 CE2 CZ2 135.7
CE2 CZ2 CH2 120.0
CZ2 CH2 CZ3 120.0
CH2 CZ3 CE3 120.0
CZ3 CE3 CD2 120.0
CE2 CD2 CE3 120.0
CD2 CE2 CZ2 120.0
CE3 CD2 CG 131.5
CG CD1 HD1 124.6
HD1 CD1 NE1 125.7
CD1 NE1 HE1 122.7
HE1 NE1 CE2 125.6
CZ3 CE3 HE3 120.0
HE3 CE3 CD2 120.0
CE2 CZ2 HZ2 120.0
HZ2 CZ2 CH2 120.0
CH2 CZ3 HZ3 120.0
HZ3 CZ3 CE3 120.0
CZ2 CH2 HH2 120.0
HH2 CH2 CZ3 120.0
[ HISD ] ; angles from MD sim, corrected to be perfectly planar
CG ND1 0.1381
ND1 CE1 0.1343
CE1 NE2 0.1335
NE2 CD2 0.1394
CD2 CG 0.137
ND1 HD1 0.101
CE1 HE1 0.108
CD2 HD2 0.108
CG ND1 CE1 107.4
ND1 CE1 NE2 113.1
CE1 NE2 CD2 104.5
NE2 CD2 CG 109.3
CD2 CG ND1 105.7
CG ND1 HD1 127.7
HD1 ND1 CE1 124.9
ND1 CE1 HE1 122.9
HE1 CE1 NE2 124.0
CG CD2 HD2 129.0
HD2 CD2 NE2 121.7
[ HISE ] ; angles from MD sim, corrected to be perfectly planar
CG ND1 0.1394
ND1 CE1 0.1335
CE1 NE2 0.1343
NE2 CD2 0.1381
CD2 CG 0.137
CD2 HD2 0.108
CE1 HE1 0.108
NE2 HE2 0.101
CG ND1 CE1 104.9
ND1 CE1 NE2 112.9
CE1 NE2 CD2 107.3
NE2 CD2 CG 106.4
CD2 CG ND1 108.5
NE2 CD2 HD2 122.4
HD2 CD2 CG 131.2
ND1 CE1 HE1 123.8
HE1 CE1 NE2 123.3
CE1 NE2 HE2 125.9
HE2 NE2 CD2 126.8
[ HISH ] ; angles from MD sim, corrected to be perfectly planar
CG ND1 0.1381
ND1 CE1 0.1343
CE1 NE2 0.1343
NE2 CD2 0.1381
CD2 CG 0.137
ND1 HD1 0.101
CE1 HE1 0.108
CD2 HD2 0.108
NE2 HE2 0.101
CG ND1 CE1 107.4
ND1 CE1 NE2 111.4
CE1 NE2 CD2 107.2
NE2 CD2 CG 107.4
CD2 CG ND1 106.6
CG ND1 HD1 127.4
HD1 ND1 CE1 125.2
ND1 CE1 HE1 124.3
HE1 CE1 NE2 124.3
CE1 NE2 HE2 126.4
HE2 NE2 CD2 126.4
NE2 CD2 HD2 120.8
HD2 CD2 CG 131.8
|