| blob | f37d7d706cccdd7c5b54aa07f567e61e672ff1b7 |
1 ; Amber forcefield converted to Gromacs
2 ; from file /usr/slocal/amber6/dat/parm98.dat
4 ; PARM94 for DNA, RNA and proteins with TIP3P Water. USE SCEE=1.2 in energy progs
5 ;
7 [ bondtypes ]
8 ; ai aj ft b0 kb
9 ; (nm) (kj/mol/nm2)
10 OW HW 1 0.09572 231530 ; TIP3P water
11 HW HW 1 0.15136 231530 ; TIP3P water
12 C CA 1 0.1409 196361 ; JCC,7,(1986),230; TYR
13 C CB 1 0.1419 187150 ; JCC,7,(1986),230; GUA
14 C CM 1 0.1444 171659 ; JCC,7,(1986),230; THY,URA
15 C CT 1 0.1522 132722 ; JCC,7,(1986),230; AA
16 C N* 1 0.1383 177520 ; JCC,7,(1986),230; CYT,URA
17 C NA 1 0.1388 175008 ; JCC,7,(1986),230; GUA.URA
18 C NC 1 0.1358 191337 ; JCC,7,(1986),230; CYT
19 C O 1 0.1229 238648 ; JCC,7,(1986),230; AA,CYT,GUA,THY,URA
20 C O2 1 0.125 274654 ; JCC,7,(1986),230; GLU,ASP
21 C OH 1 0.1364 188406 ; JCC,7,(1986),230; TYR
22 CA CA 1 0.14 196361 ; JCC,7,(1986),230; BENZENE,PHE,TRP,TYR
23 CA CB 1 0.1404 196361 ; JCC,7,(1986),230; ADE,TRP
24 CA CM 1 0.1433 178776 ; JCC,7,(1986),230; CYT
25 CA CT 1 0.151 132722 ; JCC,7,(1986),230; PHE,TYR
26 CA HA 1 0.108 153656 ; changed from 340. bsd on C6H6 nmodes; PHE,TRP,TYR
27 CA H4 1 0.108 153656 ; changed from 340. bsd on C6H6 nmodes; no assigned
28 CA N2 1 0.134 201385 ; JCC,7,(1986),230; ARG,CYT,GUA
29 CA NA 1 0.1381 178776 ; JCC,7,(1986),230; GUA
30 CA NC 1 0.1339 202222 ; JCC,7,(1986),230; ADE,CYT,GUA
31 CB CB 1 0.137 217714 ; JCC,7,(1986),230; ADE,GUA
32 CB N* 1 0.1374 182544 ; JCC,7,(1986),230; ADE,GUA
33 CB NB 1 0.1391 173334 ; JCC,7,(1986),230; ADE,GUA
34 CB NC 1 0.1354 193011 ; JCC,7,(1986),230; ADE,GUA
35 CK H5 1 0.108 153656 ; changed from 340. bsd on C6H6 nmodes; ADE,GUA
36 CK N* 1 0.1371 184219 ; JCC,7,(1986),230; ADE,GUA
37 CK NB 1 0.1304 221482 ; JCC,7,(1986),230; ADE,GUA
38 CM CM 1 0.135 229855 ; JCC,7,(1986),230; CYT,THY,URA
39 CM CT 1 0.151 132722 ; JCC,7,(1986),230; THY
40 CM HA 1 0.108 153656 ; changed from 340. bsd on C6H6 nmodes; CYT,URA
41 CM H4 1 0.108 153656 ; changed from 340. bsd on C6H6 nmodes; CYT,URA
42 CM H5 1 0.108 153656 ; changed from 340. bsd on C6H6 nmodes; not assigned
43 CM N* 1 0.1365 187569 ; JCC,7,(1986),230; CYT,THY,URA
44 CQ H5 1 0.108 153656 ; changed from 340. bsd on C6H6 nmodes; ADE
45 CQ NC 1 0.1324 210177 ; JCC,7,(1986),230; ADE
46 CT CT 1 0.1526 129791 ; JCC,7,(1986),230; AA, SUGARS
47 CT HC 1 0.109 142351 ; changed from 331 bsd on NMA nmodes; AA, SUGARS
48 CT H1 1 0.109 142351 ; changed from 331 bsd on NMA nmodes; AA, RIBOSE
49 CT H2 1 0.109 142351 ; changed from 331 bsd on NMA nmodes; SUGARS
50 CT H3 1 0.109 142351 ; changed from 331 bsd on NMA nmodes; not assigned
51 CT HP 1 0.109 142351 ; changed from 331; AA-lysine, methyl ammonium cation
52 CT N* 1 0.1475 141095 ; JCC,7,(1986),230; ADE,CYT,GUA,THY,URA
53 CT N2 1 0.1463 141095 ; JCC,7,(1986),230; ARG
54 CT OH 1 0.141 133978 ; JCC,7,(1986),230; SUGARS
55 CT OS 1 0.141 133978 ; JCC,7,(1986),230; NUCLEIC ACIDS
56 H N2 1 0.101 181707 ; JCC,7,(1986),230; ADE,CYT,GUA,ARG
57 H N* 1 0.101 181707 ; for plain unmethylated bases ADE,CYT,GUA,ARG
58 H NA 1 0.101 181707 ; JCC,7,(1986),230; GUA,URA,HIS
59 HO OH 1 0.096 231530 ; JCC,7,(1986),230; SUGARS,SER,TYR
60 HO OS 1 0.096 231530 ; JCC,7,(1986),230; NUCLEOTIDE ENDS
61 O2 P 1 0.148 219807 ; JCC,7,(1986),230; NA PHOSPHATES
62 OH P 1 0.161 96296.4 ; JCC,7,(1986),230; NA PHOSPHATES
63 OS P 1 0.161 96296.4 ; JCC,7,(1986),230; NA PHOSPHATES
64 C* HC 1 0.108 153656 ; changed from 340. bsd on C6H6 nmodes, not needed AA
65 C N 1 0.1335 205153 ; JCC,7,(1986),230; AA
66 C* CB 1 0.1459 162448 ; JCC,7,(1986),230; TRP
67 C* CT 1 0.1495 132722 ; JCC,7,(1986),230; TRP
68 C* CW 1 0.1352 228599 ; JCC,7,(1986),230; TRP
69 CA CN 1 0.14 196361 ; JCC,7,(1986),230; TRP
70 CB CN 1 0.1419 187150 ; JCC,7,(1986),230; TRP
71 CC CT 1 0.1504 132722 ; JCC,7,(1986),230; HIS
72 CC CV 1 0.1375 214364 ; JCC,7,(1986),230; HIS(delta)
73 CC CW 1 0.1371 216876 ; JCC,7,(1986),230; HIS(epsilon)
74 CC NA 1 0.1385 176683 ; JCC,7,(1986),230; HIS
75 CC NB 1 0.1394 171659 ; JCC,7,(1986),230; HIS
76 CN NA 1 0.138 179195 ; JCC,7,(1986),230; TRP
77 CR H5 1 0.108 153656 ; changed from 340. bsd on C6H6 nmodes;HIS
78 CR NA 1 0.1343 199710 ; JCC,7,(1986),230; HIS
79 CR NB 1 0.1335 204316 ; JCC,7,(1986),230; HIS
80 CT N 1 0.1449 141095 ; JCC,7,(1986),230; AA
81 CT N3 1 0.1471 153656 ; JCC,7,(1986),230; LYS
82 CT S 1 0.181 95040.4 ; changed from 222.0 based on dimethylS nmodes
83 CT SH 1 0.181 99227.2 ; changed from 222.0 based on methanethiol nmodes
84 CV H4 1 0.108 153656 ; changed from 340. bsd on C6H6 nmodes; HIS
85 CV NB 1 0.1394 171659 ; JCC,7,(1986),230; HIS
86 CW H4 1 0.108 153656 ; changed from 340. bsd on C6H6 nmodes;HIS(epsilon,+)
87 CW NA 1 0.1381 178776 ; JCC,7,(1986),230; HIS,TRP
88 H N 1 0.101 181707 ; JCC,7,(1986),230; AA
89 H N3 1 0.101 181707 ; JCC,7,(1986),230; LYS
90 HS SH 1 0.1336 114718 ; JCC,7,(1986),230; CYS
91 S S 1 0.2038 69500.9 ; JCC,7,(1986),230; CYX (SCHERAGA)
92 CT F 1 0.138 153656 ; JCC,13,(1992),963;CF4; R0=1.332 FOR CHF3
94 [ angletypes ]
95 ; ai aj ak ft th0 cth
96 ; (degr) (kj/mol/rad2)
97 HW OW HW 1 104.52 418.68 ; TIP3P water
98 HW HW OW 1 127.74 0 ; (found in crystallographic water with 3 bonds)
99 CB C NA 1 111.3 293.076 ; NA
100 CB C O 1 128.8 334.944 ;
101 CM C NA 1 114.1 293.076 ;
102 CM C O 1 125.3 334.944 ;
103 CT C O 1 120.4 334.944 ;
104 CT C O2 1 117 293.076 ;
105 CT C OH 1 117 293.076 ;
106 N* C NA 1 115.4 293.076 ;
107 N* C NC 1 118.6 293.076 ;
108 N* C O 1 120.9 334.944 ;
109 NA C O 1 120.6 334.944 ;
110 NC C O 1 122.5 334.944 ;
111 CT C N 1 116.6 293.076 ; AA general
112 N C O 1 122.9 334.944 ; AA general
113 O C O 1 126 334.944 ; AA COO- terminal residues
114 O2 C O2 1 126 334.944 ; AA GLU (SCH JPC 79,2379)
115 O C OH 1 126 334.944 ;
116 CA C CA 1 120 263.768 ; changed from 85.0 bsd on C6H6 nmodes; AA tyr
117 CA C OH 1 120 293.076 ; AA tyr
118 C CA CA 1 120 263.768 ; changed from 85.0 bsd on C6H6 nmodes
119 CA CA CA 1 120 263.768 ; changed from 85.0 bsd on C6H6 nmodes
120 CA CA CB 1 120 263.768 ; changed from 85.0 bsd on C6H6 nmodes
121 CA CA CT 1 120 293.076 ;
122 CA CA HA 1 120 146.538 ;
123 CA CA H4 1 120 146.538 ;
124 CB CA HA 1 120 146.538 ;
125 CB CA H4 1 120 146.538 ;
126 CB CA N2 1 123.5 293.076 ;
127 CB CA NC 1 117.3 293.076 ;
128 CM CA N2 1 120.1 293.076 ;
129 CM CA NC 1 121.5 293.076 ;
130 N2 CA NA 1 116 293.076 ;
131 N2 CA NC 1 119.3 293.076 ;
132 NA CA NC 1 123.3 293.076 ;
133 C CA HA 1 120 146.538 ; AA tyr
134 N2 CA N2 1 120 293.076 ; AA arg
135 CN CA HA 1 120 146.538 ; AA trp
136 CA CA CN 1 120 263.768 ; changed from 85.0 bsd on C6H6 nmodes; AA trp
137 C CB CB 1 119.2 263.768 ; changed from 85.0 bsd on C6H6 nmodes; NA gua
138 C CB NB 1 130 293.076 ;
139 CA CB CB 1 117.3 263.768 ; changed from 85.0 bsd on C6H6 nmodes; NA ade
140 CA CB NB 1 132.4 293.076 ;
141 CB CB N* 1 106.2 293.076 ;
142 CB CB NB 1 110.4 293.076 ;
143 CB CB NC 1 127.7 293.076 ;
144 N* CB NC 1 126.2 293.076 ;
145 C* CB CA 1 134.9 263.768 ; changed from 85.0 bsd on C6H6 nmodes; AA trp
146 C* CB CN 1 108.8 263.768 ; changed from 85.0 bsd on C6H6 nmodes; AA trp
147 CA CB CN 1 116.2 263.768 ; changed from 85.0 bsd on C6H6 nmodes; AA trp
148 H5 CK N* 1 123.05 146.538 ;
149 H5 CK NB 1 123.05 146.538 ;
150 N* CK NB 1 113.9 293.076 ;
151 C CM CM 1 120.7 263.768 ; changed from 85.0 bsd on C6H6 nmodes; NA thy
152 C CM CT 1 119.7 293.076 ;
153 C CM HA 1 119.7 146.538 ;
154 C CM H4 1 119.7 146.538 ;
155 CA CM CM 1 117 263.768 ; changed from 85.0 bsd on C6H6 nmodes; NA cyt
156 CA CM HA 1 123.3 146.538 ;
157 CA CM H4 1 123.3 146.538 ;
158 CM CM CT 1 119.7 293.076 ;
159 CM CM HA 1 119.7 146.538 ;
160 CM CM H4 1 119.7 146.538 ;
161 CM CM N* 1 121.2 293.076 ;
162 H4 CM N* 1 119.1 146.538 ;
163 H5 CQ NC 1 115.45 146.538 ;
164 NC CQ NC 1 129.1 293.076 ;
165 CM CT HC 1 109.5 209.34 ; changed based on NMA nmodes
166 CT CT CT 1 109.5 167.472 ;
167 CT CT HC 1 109.5 209.34 ; changed based on NMA nmodes
168 CT CT H1 1 109.5 209.34 ; changed based on NMA nmodes
169 CT CT H2 1 109.5 209.34 ; changed based on NMA nmodes
170 CT CT HP 1 109.5 209.34 ; changed based on NMA nmodes
171 CT CT N* 1 109.5 209.34 ;
172 CT CT OH 1 109.5 209.34 ;
173 CT CT OS 1 109.5 209.34 ;
174 HC CT HC 1 109.5 146.538 ;
175 H1 CT H1 1 109.5 146.538 ;
176 HP CT HP 1 109.5 146.538 ; AA lys, ch3nh4+
177 H2 CT N* 1 109.5 209.34 ; changed based on NMA nmodes
178 H1 CT N* 1 109.5 209.34 ; changed based on NMA nmodes
179 H1 CT OH 1 109.5 209.34 ; changed based on NMA nmodes
180 H1 CT OS 1 109.5 209.34 ; changed based on NMA nmodes
181 H2 CT OS 1 109.5 209.34 ; changed based on NMA nmodes
182 N* CT OS 1 109.5 209.34 ;
183 H1 CT N 1 109.5 209.34 ; AA general changed based on NMA nmodes
184 C CT H1 1 109.5 209.34 ; AA general changed based on NMA nmodes
185 C CT HP 1 109.5 209.34 ; AA zwitterion changed based on NMA nmodes
186 H1 CT S 1 109.5 209.34 ; AA cys changed based on NMA nmodes
187 H1 CT SH 1 109.5 209.34 ; AA cyx changed based on NMA nmodes
188 CT CT S 1 114.7 209.34 ; AA cyx (SCHERAGA JPC 79,1428)
189 CT CT SH 1 108.6 209.34 ; AA cys
190 H2 CT H2 1 109.5 146.538 ; AA lys
191 H1 CT N2 1 109.5 209.34 ; AA arg changed based on NMA nmodes
192 HP CT N3 1 109.5 209.34 ; AA lys, ch3nh3+, changed based on NMA nmodes
193 CA CT CT 1 114 263.768 ; AA phe tyr (SCH JPC 79,2379)
194 C CT HC 1 109.5 209.34 ; AA gln changed based on NMA nmodes
195 C CT N 1 110.1 263.768 ; AA general
196 CT CT N2 1 111.2 334.944 ; AA arg (JCP 76, 1439)
197 CT CT N 1 109.7 334.944 ; AA ala, general (JACS 94, 2657)
198 C CT CT 1 111.1 263.768 ; AA general
199 CA CT HC 1 109.5 209.34 ; AA tyr changed based on NMA nmodes
200 CT CT N3 1 111.2 334.944 ; AA lys (JCP 76, 1439)
201 CC CT CT 1 113.1 263.768 ; AA his
202 CC CT HC 1 109.5 209.34 ; AA his changed based on NMA nmodes
203 C CT N3 1 111.2 334.944 ; AA amino terminal residues
204 C* CT CT 1 115.6 263.768 ; AA trp
205 C* CT HC 1 109.5 209.34 ; AA trp changed based on NMA nmodes
206 CT CC NA 1 120 293.076 ; AA his
207 CT CC CV 1 120 293.076 ; AA his
208 CT CC NB 1 120 293.076 ; AA his
209 CV CC NA 1 120 293.076 ; AA his
210 CW CC NA 1 120 293.076 ; AA his
211 CW CC NB 1 120 293.076 ; AA his
212 CT CC CW 1 120 293.076 ; AA his
213 H5 CR NA 1 120 146.538 ; AA his
214 H5 CR NB 1 120 146.538 ; AA his
215 NA CR NA 1 120 293.076 ; AA his
216 NA CR NB 1 120 293.076 ; AA his
217 CC CV H4 1 120 146.538 ; AA his
218 CC CV NB 1 120 293.076 ; AA his
219 H4 CV NB 1 120 146.538 ; AA his
220 CC CW H4 1 120 146.538 ; AA his
221 CC CW NA 1 120 293.076 ; AA his
222 H4 CW NA 1 120 146.538 ; AA his
223 C* CW H4 1 120 146.538 ; AA trp
224 C* CW NA 1 108.7 293.076 ; AA trp
225 CT C* CW 1 125 293.076 ; AA trp
226 CB C* CT 1 128.6 293.076 ; AA trp
227 CB C* CW 1 106.4 263.768 ; changed from 85.0 bsd on C6H6 nmodes; AA trp
228 CA CN NA 1 132.8 293.076 ; AA trp
229 CB CN NA 1 104.4 293.076 ; AA trp
230 CA CN CB 1 122.7 263.768 ; changed from 85.0 bsd on C6H6 nmodes; AA trp
231 C N CT 1 121.9 209.34 ; AA general
232 C N H 1 120 125.604 ; AA general, gln, asn,changed based on NMA nmodes
233 CT N H 1 118.04 125.604 ; AA general, changed based on NMA nmodes
234 CT N CT 1 118 209.34 ; AA pro (DETAR JACS 99,1232)
235 H N H 1 120 146.538 ; ade,cyt,gua,gln,asn **
236 C N* CM 1 121.6 293.076 ;
237 C N* CT 1 117.6 293.076 ;
238 C N* H 1 119.2 125.604 ; changed based on NMA nmodes
239 CB N* CK 1 105.4 293.076 ;
240 CB N* CT 1 125.8 293.076 ;
241 CB N* H 1 125.8 125.604 ; for unmethylated n.a. bases,chngd bsd NMA nmodes
242 CK N* CT 1 128.8 293.076 ;
243 CK N* H 1 128.8 125.604 ; for unmethylated n.a. bases,chngd bsd NMA nmodes
244 CM N* CT 1 121.2 293.076 ;
245 CM N* H 1 121.2 125.604 ; for unmethylated n.a. bases,chngd bsd NMA nmodes
246 CA N2 H 1 120 146.538 ;
247 H N2 H 1 120 146.538 ;
248 CT N2 H 1 118.4 146.538 ; AA arg
249 CA N2 CT 1 123.2 209.34 ; AA arg
250 CT N3 H 1 109.5 209.34 ; AA lys, changed based on NMA nmodes
251 CT N3 CT 1 109.5 209.34 ; AA pro/nt
252 H N3 H 1 109.5 146.538 ; AA lys, AA(end)
253 C NA C 1 126.4 293.076 ;
254 C NA CA 1 125.2 293.076 ;
255 C NA H 1 116.8 125.604 ; changed based on NMA nmodes
256 CA NA H 1 118 125.604 ; changed based on NMA nmodes
257 CC NA CR 1 120 293.076 ; AA his
258 CC NA H 1 120 125.604 ; AA his, changed based on NMA nmodes
259 CR NA CW 1 120 293.076 ; AA his
260 CR NA H 1 120 125.604 ; AA his, changed based on NMA nmodes
261 CW NA H 1 120 125.604 ; AA his, changed based on NMA nmodes
262 CN NA CW 1 111.6 293.076 ; AA trp
263 CN NA H 1 123.1 125.604 ; AA trp, changed based on NMA nmodes
264 CB NB CK 1 103.8 293.076 ;
265 CC NB CR 1 117 293.076 ; AA his
266 CR NB CV 1 117 293.076 ; AA his
267 C NC CA 1 120.5 293.076 ;
268 CA NC CB 1 112.2 293.076 ;
269 CA NC CQ 1 118.6 293.076 ;
270 CB NC CQ 1 111 293.076 ;
271 C OH HO 1 113 146.538 ;
272 CT OH HO 1 108.5 230.274 ;
273 HO OH P 1 108.5 188.406 ;
274 CT OS CT 1 109.5 251.208 ;
275 CT OS P 1 120.5 418.68 ;
276 P OS P 1 120.5 418.68 ;
277 O2 P OH 1 108.23 188.406 ;
278 O2 P O2 1 119.9 586.152 ;
279 O2 P OS 1 108.23 418.68 ;
280 OH P OS 1 102.6 188.406 ;
281 OS P OS 1 102.6 188.406 ;
282 CT S CT 1 98.9 259.582 ; AA met
283 CT S S 1 103.7 284.702 ; AA cyx (SCHERAGA JPC 79,1428)
284 CT SH HS 1 96 180.032 ; changed from 44.0 based on methanethiol nmodes
285 HS SH HS 1 92.07 146.538 ; AA cys
286 F CT F 1 109.1 322.384 ; JCC,13,(1992),963;
287 F CT H1 1 109.5 146.538 ; JCC,13,(1992),963;
289 [ dihedraltypes ]
290 ; aj ak ft phi0 cp mult
291 ; (degr) (kJ/mol/rad)
292 C CA 1 180 15.1771 2 ; intrpol.bsd.on C6H6
293 C CB 1 180 12.5604 2 ; intrpol.bsd.on C6H6
294 C CM 1 180 9.10629 2 ; intrpol.bsd.on C6H6
295 C N* 1 180 6.07086 2 ; JCC,7,(1986),230
296 C NA 1 180 5.65218 2 ; JCC,7,(1986),230
297 C NC 1 180 16.7472 2 ; JCC,7,(1986),230
298 C OH 1 180 3.76812 2 ; JCC,7,(1986),230
299 C CT 1 0 0 2 ; JCC,7,(1986),230
300 CA CA 1 180 15.1771 2 ; intrpol.bsd.on C6H6
301 CA CB 1 180 14.6538 2 ; intrpol.bsd.on C6H6
302 CA CM 1 180 10.6763 2 ; intrpol.bsd.on C6H6
303 CA CT 1 0 0 2 ; JCC,7,(1986),230
304 CA N2 1 180 10.0483 2 ; reinterpolated 93'
305 CA NA 1 180 6.2802 2 ; JCC,7,(1986),230
306 CA NC 1 180 20.0966 2 ; JCC,7,(1986),230
307 CB CB 1 180 22.8181 2 ; intrpol.bsd.on C6H6
308 CB N* 1 180 6.90822 2 ; JCC,7,(1986),230
309 CB NB 1 180 10.6763 2 ; JCC,7,(1986),230
310 CB NC 1 180 17.3752 2 ; JCC,7,(1986),230
311 CK N* 1 180 7.11756 2 ; JCC,7,(1986),230
312 CK NB 1 180 41.868 2 ; JCC,7,(1986),230
313 CM CM 1 180 27.8422 2 ; intrpol.bsd.on C6H6
314 CM CT 1 0 0 3 ; JCC,7,(1986),230
315 CM N* 1 180 7.74558 2 ; JCC,7,(1986),230
316 CQ NC 1 180 28.4702 2 ; JCC,7,(1986),230
317 CT CT 1 0 0.65128 3 ; JCC,7,(1986),230
318 CT N 1 0 0 2 ; JCC,7,(1986),230
319 CT N* 1 0 0 2 ; JCC,7,(1986),230
320 CT N2 1 0 0 3 ; JCC,7,(1986),230
321 CT OH 1 0 0.6978 3 ; JCC,7,(1986),230
322 CT OS 1 0 1.60494 3 ; JCC,7,(1986),230
323 OH P 1 0 1.0467 3 ; JCC,7,(1986),230
324 OS P 1 0 1.0467 3 ; JCC,7,(1986),230
325 C N 1 180 10.467 2 ; AA|check Wendy?&NMA
326 CT N3 1 0 0.65128 3 ; JCC,7,(1986),230
327 CT S 1 0 1.3956 3 ; JCC,7,(1986),230
328 CT SH 1 0 1.0467 3 ; JCC,7,(1986),230
329 C* CB 1 180 7.01289 2 ; intrpol.bsd.onC6H6aa
330 C* CT 1 0 0 2 ; JCC,7,(1986),230
331 C* CW 1 180 27.3189 2 ; intrpol.bsd.on C6H6
332 CA CN 1 180 15.1771 2 ; reinterpolated 93'
333 CB CN 1 180 12.5604 2 ; reinterpolated 93'
334 CC CT 1 0 0 2 ; JCC,7,(1986),230
335 CC CV 1 180 21.562 2 ; intrpol.bsd.on C6H6
336 CC CW 1 180 22.504 2 ; intrpol.bsd.on C6H6
337 CC NA 1 180 5.86152 2 ; JCC,7,(1986),230
338 CC NB 1 180 10.0483 2 ; JCC,7,(1986),230
339 CN NA 1 180 6.38487 2 ; reinterpolated 93'
340 CR NA 1 180 9.73431 2 ; JCC,7,(1986),230
341 CR NB 1 180 20.934 2 ; JCC,7,(1986),230
342 CV NB 1 180 10.0483 2 ; JCC,7,(1986),230
343 CW NA 1 180 6.2802 2 ; JCC,7,(1986),230
345 ; defining dihedral parameters for four-atom dependent
346 ; dihedral types, which Gromacs does not handle by default
347 #define ad_CT_CT_OS_CT_1 0 1.60354 3 0 1.60354 3
348 #define ad_CT_CT_OS_CT_2 180 0.41868 2 180 0.41868 2
349 #define ad_CT_OS_CT_N*_1 0 1.60354 3 0 1.60354 3
350 #define ad_CT_OS_CT_N*_2 0 4.1868 2 0 4.1868 2
351 #define ad_C__N__CT_C_ 180 0.83736 2 180 0.83736 2
352 #define ad_N__CT_C__N__1 180 1.67472 4 180 1.67472 4
353 #define ad_N__CT_C__N__2 180 5.65218 2 180 5.65218 2
354 #define ad_N__CT_C__N__3 180 3.1401 1 180 3.1401 1
355 #define ad_CT_CT_N__C__1 180 2.0934 4 180 2.0934 4
356 #define ad_CT_CT_N__C__2 180 0.62802 3 180 0.62802 3
357 #define ad_CT_CT_N__C__3 0 2.219 1 0 2.219 1
358 #define ad_CT_CT_C__N__1 0 0.41868 4 0 0.41868 4
359 #define ad_CT_CT_C__N__2 0 0.293076 2 0 0.293076 2
360 #define ad_H__N__C__O__1 180 10.467 2 180 10.467 2 ; JCC,7,(1986),230
361 #define ad_H__N__C__O__2 0 8.3736 1 0 8.3736 1 ; J.C.cistrans-NMA DE
362 #define ad_CT_S__S__CT_1 0 14.6538 2 0 14.6538 2 ; JCC,7,(1986),230
363 #define ad_CT_S__S__CT_2 0 2.51208 3 0 2.51208 3 ; JCC,7,(1986),230
364 #define ad_OS_CT_CT_OS_1 0 0.602899 3 0 0.602899 3 ; JCC,7,(1986),230
365 #define ad_OS_CT_CT_OS_2 0 6.2802 2 0 6.2802 2 ; pucker anal (93')
366 #define ad_OS_CT_CT_OH_1 0 0.602899 3 0 0.602899 3 ; JCC,7,(1986),230
367 #define ad_OS_CT_CT_OH_2 0 6.2802 2 0 6.2802 2 ; pucker anal (93')
368 #define ad_OH_CT_CT_OH_1 0 0.602899 3 0 0.602899 3 ; JCC,7,(1986),230
369 #define ad_OH_CT_CT_OH_2 0 6.2802 2 0 6.2802 2 ; check glicolWC? puc
370 #define ad_OH_P__OS_CT_1 0 1.0467 3 0 1.0467 3 ; JCC,7,(1986),230
371 #define ad_OH_P__OS_CT_2 0 5.02416 2 0 5.02416 2 ; gg> ene.631g*/mp2
372 #define ad_OS_P__OS_CT_1 0 1.0467 3 0 1.0467 3 ; JCC,7,(1986),230
373 #define ad_OS_P__OS_CT_2 0 5.02416 2 0 5.02416 2 ; gg> ene.631g*/mp2
374 #define ad_OS_CT_N*_CK_1 0 0 2 0 0 2 ; sugar frag calc (PC)
375 #define ad_OS_CT_N*_CK_2 0 10.467 1 0 10.467 1 ; sugar frag calc (PC)
376 #define ad_OS_CT_N*_CM_1 0 0 2 0 0 2 ; sugar frag calc (PC)
377 #define ad_OS_CT_N*_CM_2 0 10.467 1 0 10.467 1 ; sugar frag calc (PC)
379 ; ai aj ak al ft q0 cq mult
380 ; WARNING: using Gromacs propers to define Amber impropers
381 ; defining improper parameters for improper types
382 #define ai_X__X__C__O_ 43.9614 180 2 43.9614 180 2 ; JCC,7,(1986),230
383 #define ai_X__O2_C__O2 43.9614 180 2 43.9614 180 2 ; JCC,7,(1986),230
384 #define ai_X__X__N__H_ 4.1868 180 2 4.1868 180 2 ; JCC,7,(1986),230
385 #define ai_X__X__N2_H_ 4.1868 180 2 4.1868 180 2 ; JCC,7,(1986),230
386 #define ai_X__X__NA_H_ 4.1868 180 2 4.1868 180 2 ; JCC,7,(1986),230
387 #define ai_X__N2_CA_N2 43.9614 180 2 43.9614 180 2 ; JCC,7,(1986),230
388 #define ai_X__CT_N__CT 4.1868 180 2 4.1868 180 2 ; JCC,7,(1986),230
389 #define ai_X__X__CA_HA 4.60548 180 2 4.60548 180 2 ; bsd.on C6H6 nmodes
390 #define ai_X__X__CW_H4 4.60548 180 2 4.60548 180 2
391 #define ai_X__X__CR_H5 4.60548 180 2 4.60548 180 2
392 #define ai_X__X__CV_H4 4.60548 180 2 4.60548 180 2
393 #define ai_X__X__CQ_H5 4.60548 180 2 4.60548 180 2
394 #define ai_X__X__CK_H5 4.60548 180 2 4.60548 180 2
395 #define ai_X__X__CM_H4 4.60548 180 2 4.60548 180 2
396 #define ai_X__X__CM_HA 4.60548 180 2 4.60548 180 2
397 #define ai_X__X__CA_H4 4.60548 180 2 4.60548 180 2 ; bsd.on C6H6 nmodes
398 #define ai_X__X__CA_H5 4.60548 180 2 4.60548 180 2 ; bsd.on C6H6 nmodes
399 #define ai_CK_CB_N*_CT 4.1868 180 2 4.1868 180 2
400 #define ai_CM_C__N*_CT 4.1868 180 2 4.1868 180 2 ; dac guess, 9/94
401 #define ai_CM_C__CM_CT 4.60548 180 2 4.60548 180 2
402 #define ai_CT_O__C__OH 43.9614 180 2 43.9614 180 2
403 #define ai_NA_CV_CC_CT 4.60548 180 2 4.60548 180 2
404 #define ai_NB_CW_CC_CT 4.60548 180 2 4.60548 180 2
405 #define ai_NA_CW_CC_CT 4.60548 180 2 4.60548 180 2
406 #define ai_CW_CB_C*_CT 4.60548 180 2 4.60548 180 2
407 #define ai_CA_CA_CA_CT 4.60548 180 2 4.60548 180 2
408 #define ai_C__CM_CM_CT 4.60548 180 2 4.60548 180 2 ; dac guess, 9/94
409 #define ai_NC_CM_CA_N2 4.60548 180 2 4.60548 180 2 ; dac guess, 9/94
410 #define ai_CB_NC_CA_N2 4.60548 180 2 4.60548 180 2 ; dac, 10/94
411 #define ai_NA_NC_CA_N2 4.60548 180 2 4.60548 180 2 ; dac, 10/94
412 #define ai_CA_CA_C__OH 4.60548 180 2 4.60548 180 2
414 ; Found:
415 ; # bonds: 83
416 ; # angles: 191
417 ; # propers: 83
418 ; # impropers: 31