| blob | a1491025ff8dcb0415227a16f64007cd850b8fe3 |
1 ;
2 ; Force field based on GROMOS with new charges as described in
3 ; D. van der Spoel, K.A. Feenstra, M.A. Hemminga and H.J.C. Berendsen:
4 ; Molecular modeling of the RNA binding N-terminal part of cowpea chlorotic
5 ; mottle virus coat protein in solution with phosphate ions
6 ; Biophys. J. 71 pp. 2920-2932 (1996)
7 ;
8 ; Octa Phosphate h2p8o25(5-)
9 ; Anton Feenstra, June 23 '95
10 ; based on ab-initio full geometry opt. by Gaussian '92 on tetra phosphate
11 ; charge densities by Gaussian '92
12 ; Gaussian '92 output manually symmetrized and muliplied (and adjusted)
13 ;
14 ; 4 5 8 9 12 13 16 17 20 21 24 25 28 29 32 33
15 ; \ / \ / \ / \ / \ / \ / \ / \ /
16 ; 1 7 11 15 19 23 27 31
17 ; / \ / \ / \ / \ / \ / \ / \ / \
18 ; 3-2 6 10 14 18 22 26 30 34-35
19 ;
20 ; * * * * * * *
21 ; OM OM*OM OM*OM OM*OM OM*OM OM*OM OM*OM OM*OM OM
22 ; \ / * \ / * \ / * \ / * \ / * \ / * \ / * \ /
23 ; P1 * P2 * P2 * P2 * * P2 * P2 * P2 * P1
24 ; / \ / \ / \ / \ / \ / \ / \ / \
25 ; HO-OA *OS1 *OS2 *OS2 *OS2* OS2* OS2* OS1* OA-HO
26 ; * * * * * * * *
27 ; 1 * 2 * 3 * 4 * 5 * 6 * 7 * 8 * 9
28 ;
29 ; charge groups (see * above)
30 ; [HPO3] [PO3] [PO3] .. [O] .. [PO3] [PO3] [PO3H]
31 ; -0.59 -0.97 -0.97 .. -0.88 .. -0.97 -0.97 -0.59
32 ;
33 ; bond-lengths: angles: dihedrals:
34 ; P-OM 0.155 OA-P-OS 97 H-OA-P-OS 3
35 ; P-OS 0.165 OS-P-OS 102 OA-P-OS-P -19
36 ; P-OA 0.164 OS-P-OM 109 OS-P-OS-P -222 / -147
37 ; OA-H 0.101 OA-P-OM 110
39 ; !!! ATTENTION: file has not (yet) been tested in simulation !!!
41 [ moleculetype ]
42 ; name nrexcl
43 h2p8o25 3
45 [ atoms ]
46 ; nr type resnr residu atom cgnr charge mass
47 1 P 1 PI P1 1 1.85
48 2 OA 1 PI O2 1 -1.02
49 3 HO 1 PI H3 1 0.58
50 4 OM 1 PI O4 1 -1.0
51 5 OM 1 PI O5 1 -1.0
52 6 OS 1 PI O6 2 -0.92
53 7 P 1 PI P7 2 1.95
54 8 OM 1 PI O8 2 -1.0
55 9 OM 1 PI O9 2 -1.0
56 10 OS 1 PI O10 3 -0.88
57 11 P 1 PI P11 3 1.95
58 12 OM 1 PI O12 3 -1.0
59 13 OM 1 PI O13 3 -1.0
60 14 OS 1 PI O14 4 -0.88
61 15 P 1 PI P15 4 1.95
62 16 OM 1 PI O16 4 -1.0
63 17 OM 1 PI O17 4 -1.0
64 18 OS 1 PI O18 5 -0.88
65 19 P 1 PI P19 6 1.95
66 20 OM 1 PI O20 6 -1.0
67 21 OM 1 PI O21 6 -1.0
68 22 OS 1 PI O22 6 -0.88
69 23 P 1 PI P23 7 1.95
70 24 OM 1 PI O24 7 -1.0
71 25 OM 1 PI O25 7 -1.0
72 26 OS 1 PI O26 7 -0.88
73 27 P 1 PI P27 8 1.95
74 28 OM 1 PI O28 8 -1.0
75 29 OM 1 PI O29 8 -1.0
76 30 OS 1 PI O30 8 -0.92
77 31 P 1 PI P31 9 1.85
78 32 OM 1 PI O32 9 -1.0
79 33 OM 1 PI O33 9 -1.0
80 34 OA 1 PI O34 9 -1.02
81 35 HO 1 PI H35 9 0.58
83 [ bonds ]
84 ; ai aj funct c0 c1
85 2 1 1 0.164
86 3 2 1 0.101
87 4 1 1 0.155
88 5 1 1 0.155
89 6 1 1 0.165
90 7 6 1 0.165
91 8 7 1 0.155
92 9 7 1 0.155
93 10 7 1 0.165
94 11 10 1 0.165
95 12 11 1 0.155
96 13 11 1 0.155
97 14 11 1 0.165
98 15 14 1 0.165
99 16 15 1 0.155
100 17 15 1 0.155
101 18 15 1 0.165
102 19 18 1 0.165
103 20 19 1 0.155
104 21 19 1 0.155
105 22 19 1 0.165
106 23 22 1 0.165
107 24 23 1 0.155
108 25 23 1 0.155
109 26 23 1 0.165
110 27 26 1 0.165
111 28 27 1 0.155
112 29 27 1 0.155
113 30 27 1 0.165
114 31 30 1 0.165
115 32 31 1 0.155
116 33 31 1 0.155
117 34 31 1 0.164
118 35 34 1 0.101
120 [ angles ]
121 ; ai aj ak funct c0 c1
122 1 2 3 1 113.0
123 1 6 7 1 137.0 400
124 2 1 4 1 110.0
125 2 1 5 1 110.0
126 2 1 6 1 97.0
127 4 1 5 1 118.0
128 4 1 6 1 109.0
129 5 1 6 1 109.0
130 6 7 8 1 109.0
131 6 7 9 1 109.0
132 6 7 10 1 102.0
133 7 10 11 1 147.0 400
134 8 7 9 1 118.0
135 8 7 10 1 109.0
136 9 7 10 1 109.0
137 10 11 12 1 109.0
138 10 11 13 1 109.0
139 10 11 14 1 102.0
140 11 14 15 1 147.0 400
141 12 11 13 1 118.0
142 12 11 14 1 109.0
143 13 11 14 1 109.0
144 14 15 16 1 109.0
145 14 15 17 1 109.0
146 14 15 18 1 102.0
147 15 18 19 1 147.0 400
148 16 15 17 1 118.0
149 16 15 18 1 109.0
150 17 15 18 1 109.0
151 18 19 20 1 109.0
152 18 19 21 1 109.0
153 18 19 22 1 102.0
154 19 22 23 1 147.0 400
155 20 19 21 1 118.0
156 20 19 22 1 109.0
157 21 19 22 1 109.0
158 22 23 24 1 109.0
159 22 23 25 1 109.0
160 22 23 26 1 102.0
161 23 26 27 1 147.0 400
162 24 23 25 1 118.0
163 24 23 26 1 109.0
164 25 23 26 1 109.0
165 26 27 28 1 109.0
166 26 27 29 1 109.0
167 26 27 30 1 102.0
168 27 30 31 1 137.0 400
169 28 27 29 1 118.0
170 28 27 30 1 109.0
171 29 27 30 1 109.0
172 30 31 32 1 109.0
173 30 31 33 1 109.0
174 30 31 34 1 97.0
175 31 34 35 1 113.0
176 32 31 33 1 118.0
177 32 31 34 1 110.0
178 33 31 34 1 110.0
180 [ dihedrals ]
181 ; ai aj ak al funct c0 c1 c2
182 6 1 2 3 1 ; 3
183 7 6 1 2 1 -19 3.0 3
184 10 7 6 1 1 -222 3.0 3
185 11 10 7 6 1 -147 3.0 3
186 14 11 10 7 1 -222 3.0 3
187 15 14 11 10 1 -147 3.0 3
188 18 15 14 11 1 -222 3.0 3
189 19 18 15 14 1 -147 3.0 3
190 22 19 18 15 1 -147 3.0 3
191 23 22 19 18 1 -222 3.0 3
192 26 23 22 19 1 -147 3.0 3
193 27 26 23 22 1 -222 3.0 3
194 30 27 26 23 1 -147 3.0 3
195 31 30 27 26 1 -222 3.0 3
196 34 31 30 27 1 -19 3.0 3
197 35 34 31 30 1 ; 3