/usr/share/gromacs/top/gmx.ff/h2p8o25.itp is in gromacs-data 4.5.5-2.
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 | ;
; Force field based on GROMOS with new charges as described in
; D. van der Spoel, K.A. Feenstra, M.A. Hemminga and H.J.C. Berendsen:
; Molecular modeling of the RNA binding N-terminal part of cowpea chlorotic
; mottle virus coat protein in solution with phosphate ions
; Biophys. J. 71 pp. 2920-2932 (1996)
;
; Octa Phosphate h2p8o25(5-)
; Anton Feenstra, June 23 '95
; based on ab-initio full geometry opt. by Gaussian '92 on tetra phosphate
; charge densities by Gaussian '92
; Gaussian '92 output manually symmetrized and muliplied (and adjusted)
;
; 4 5 8 9 12 13 16 17 20 21 24 25 28 29 32 33
; \ / \ / \ / \ / \ / \ / \ / \ /
; 1 7 11 15 19 23 27 31
; / \ / \ / \ / \ / \ / \ / \ / \
; 3-2 6 10 14 18 22 26 30 34-35
;
; * * * * * * *
; OM OM*OM OM*OM OM*OM OM*OM OM*OM OM*OM OM*OM OM
; \ / * \ / * \ / * \ / * \ / * \ / * \ / * \ /
; P1 * P2 * P2 * P2 * * P2 * P2 * P2 * P1
; / \ / \ / \ / \ / \ / \ / \ / \
; HO-OA *OS1 *OS2 *OS2 *OS2* OS2* OS2* OS1* OA-HO
; * * * * * * * *
; 1 * 2 * 3 * 4 * 5 * 6 * 7 * 8 * 9
;
; charge groups (see * above)
; [HPO3] [PO3] [PO3] .. [O] .. [PO3] [PO3] [PO3H]
; -0.59 -0.97 -0.97 .. -0.88 .. -0.97 -0.97 -0.59
;
; bond-lengths: angles: dihedrals:
; P-OM 0.155 OA-P-OS 97 H-OA-P-OS 3
; P-OS 0.165 OS-P-OS 102 OA-P-OS-P -19
; P-OA 0.164 OS-P-OM 109 OS-P-OS-P -222 / -147
; OA-H 0.101 OA-P-OM 110
; !!! ATTENTION: file has not (yet) been tested in simulation !!!
[ moleculetype ]
; name nrexcl
h2p8o25 3
[ atoms ]
; nr type resnr residu atom cgnr charge mass
1 P 1 PI P1 1 1.85
2 OA 1 PI O2 1 -1.02
3 HO 1 PI H3 1 0.58
4 OM 1 PI O4 1 -1.0
5 OM 1 PI O5 1 -1.0
6 OS 1 PI O6 2 -0.92
7 P 1 PI P7 2 1.95
8 OM 1 PI O8 2 -1.0
9 OM 1 PI O9 2 -1.0
10 OS 1 PI O10 3 -0.88
11 P 1 PI P11 3 1.95
12 OM 1 PI O12 3 -1.0
13 OM 1 PI O13 3 -1.0
14 OS 1 PI O14 4 -0.88
15 P 1 PI P15 4 1.95
16 OM 1 PI O16 4 -1.0
17 OM 1 PI O17 4 -1.0
18 OS 1 PI O18 5 -0.88
19 P 1 PI P19 6 1.95
20 OM 1 PI O20 6 -1.0
21 OM 1 PI O21 6 -1.0
22 OS 1 PI O22 6 -0.88
23 P 1 PI P23 7 1.95
24 OM 1 PI O24 7 -1.0
25 OM 1 PI O25 7 -1.0
26 OS 1 PI O26 7 -0.88
27 P 1 PI P27 8 1.95
28 OM 1 PI O28 8 -1.0
29 OM 1 PI O29 8 -1.0
30 OS 1 PI O30 8 -0.92
31 P 1 PI P31 9 1.85
32 OM 1 PI O32 9 -1.0
33 OM 1 PI O33 9 -1.0
34 OA 1 PI O34 9 -1.02
35 HO 1 PI H35 9 0.58
[ bonds ]
; ai aj funct c0 c1
2 1 1 0.164
3 2 1 0.101
4 1 1 0.155
5 1 1 0.155
6 1 1 0.165
7 6 1 0.165
8 7 1 0.155
9 7 1 0.155
10 7 1 0.165
11 10 1 0.165
12 11 1 0.155
13 11 1 0.155
14 11 1 0.165
15 14 1 0.165
16 15 1 0.155
17 15 1 0.155
18 15 1 0.165
19 18 1 0.165
20 19 1 0.155
21 19 1 0.155
22 19 1 0.165
23 22 1 0.165
24 23 1 0.155
25 23 1 0.155
26 23 1 0.165
27 26 1 0.165
28 27 1 0.155
29 27 1 0.155
30 27 1 0.165
31 30 1 0.165
32 31 1 0.155
33 31 1 0.155
34 31 1 0.164
35 34 1 0.101
[ angles ]
; ai aj ak funct c0 c1
1 2 3 1 113.0
1 6 7 1 137.0 400
2 1 4 1 110.0
2 1 5 1 110.0
2 1 6 1 97.0
4 1 5 1 118.0
4 1 6 1 109.0
5 1 6 1 109.0
6 7 8 1 109.0
6 7 9 1 109.0
6 7 10 1 102.0
7 10 11 1 147.0 400
8 7 9 1 118.0
8 7 10 1 109.0
9 7 10 1 109.0
10 11 12 1 109.0
10 11 13 1 109.0
10 11 14 1 102.0
11 14 15 1 147.0 400
12 11 13 1 118.0
12 11 14 1 109.0
13 11 14 1 109.0
14 15 16 1 109.0
14 15 17 1 109.0
14 15 18 1 102.0
15 18 19 1 147.0 400
16 15 17 1 118.0
16 15 18 1 109.0
17 15 18 1 109.0
18 19 20 1 109.0
18 19 21 1 109.0
18 19 22 1 102.0
19 22 23 1 147.0 400
20 19 21 1 118.0
20 19 22 1 109.0
21 19 22 1 109.0
22 23 24 1 109.0
22 23 25 1 109.0
22 23 26 1 102.0
23 26 27 1 147.0 400
24 23 25 1 118.0
24 23 26 1 109.0
25 23 26 1 109.0
26 27 28 1 109.0
26 27 29 1 109.0
26 27 30 1 102.0
27 30 31 1 137.0 400
28 27 29 1 118.0
28 27 30 1 109.0
29 27 30 1 109.0
30 31 32 1 109.0
30 31 33 1 109.0
30 31 34 1 97.0
31 34 35 1 113.0
32 31 33 1 118.0
32 31 34 1 110.0
33 31 34 1 110.0
[ dihedrals ]
; ai aj ak al funct c0 c1 c2
6 1 2 3 1 ; 3
7 6 1 2 1 -19 3.0 3
10 7 6 1 1 -222 3.0 3
11 10 7 6 1 -147 3.0 3
14 11 10 7 1 -222 3.0 3
15 14 11 10 1 -147 3.0 3
18 15 14 11 1 -222 3.0 3
19 18 15 14 1 -147 3.0 3
22 19 18 15 1 -147 3.0 3
23 22 19 18 1 -222 3.0 3
26 23 22 19 1 -147 3.0 3
27 26 23 22 1 -222 3.0 3
30 27 26 23 1 -147 3.0 3
31 30 27 26 1 -222 3.0 3
34 31 30 27 1 -19 3.0 3
35 34 31 30 1 ; 3
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