| blob | 0acff7d3c6e26c13e2086adb4ae34a673528625d |
1 [ bondtypes ]
2 ; i j func b0 kb
3 C C 1 0.1525 259408.0 ; new99
4 C OS 1 0.1323 376560.0 ; new99
5 C H4 1 0.1080 307105.6 ; new99
6 C H5 1 0.1080 307105.6 ; new99
7 CA OH 1 0.1364 376560.0 ; new99
8 CM OS 1 0.1240 401664.0 ; new99
9 Cl CT 1 0.1766 194137.6 ; new99
10 Br CT 1 0.1944 133051.2 ; new99
11 I CT 1 0.2166 123846.4 ; new99
12 F CA 1 0.1359 323004.8 ; new99
13 Cl CA 1 0.1727 161502.4 ; new99
14 I CA 1 0.2075 143092.8 ; new99
15 Br CA 1 0.1890 143929.6 ; new99
16 OW HW 1 0.09572 462750.4 ; P water
17 HW HW 1 0.15136 462750.4 ; P water
18 C CA 1 0.14090 392459.2 ; 7,(1986),230; TYR
19 C CB 1 0.14190 374049.6 ; 7,(1986),230; GUA
20 C CM 1 0.14440 343088.0 ; 7,(1986),230; THY,URA
21 C CT 1 0.15220 265265.6 ; 7,(1986),230; AA
22 C N* 1 0.13830 354803.2 ; 7,(1986),230; CYT,URA
23 C NA 1 0.13880 349782.4 ; 7,(1986),230; GUA.URA
24 C NC 1 0.13580 382417.6 ; 7,(1986),230; CYT
25 C O 1 0.12290 476976.0 ; 7,(1986),230; AA,CYT,GUA,THY,URA
26 C O2 1 0.12500 548940.8 ; 7,(1986),230; GLU,ASP
27 C OH 1 0.13640 376560.0 ; 7,(1986),230; TYR
28 CA CA 1 0.14000 392459.2 ; 7,(1986),230; BENZENE,PHE,TRP,TYR
29 CA CB 1 0.14040 392459.2 ; 7,(1986),230; ADE,TRP
30 CA CM 1 0.14330 357313.6 ; 7,(1986),230; CYT
31 CA CT 1 0.15100 265265.6 ; 7,(1986),230; PHE,TYR
32 CA HA 1 0.10800 307105.6 ; ged from 340. bsd on C6H6 nmodes; PHE,TRP,TYR
33 CA H4 1 0.10800 307105.6 ; ged from 340. bsd on C6H6 nmodes; no assigned
34 CA N2 1 0.13400 402500.8 ; 7,(1986),230; ARG,CYT,GUA
35 CA NA 1 0.13810 357313.6 ; 7,(1986),230; GUA
36 CA NC 1 0.13390 404174.4 ; 7,(1986),230; ADE,CYT,GUA
37 CB CB 1 0.13700 435136.0 ; 7,(1986),230; ADE,GUA
38 CB N* 1 0.13740 364844.8 ; 7,(1986),230; ADE,GUA
39 CB NB 1 0.13910 346435.2 ; 7,(1986),230; ADE,GUA
40 CB NC 1 0.13540 385764.8 ; 7,(1986),230; ADE,GUA
41 CK H5 1 0.10800 307105.6 ; ged from 340. bsd on C6H6 nmodes; ADE,GUA
42 CK N* 1 0.13710 368192.0 ; 7,(1986),230; ADE,GUA
43 CK NB 1 0.13040 442667.2 ; 7,(1986),230; ADE,GUA
44 CM CM 1 0.13500 459403.2 ; 7,(1986),230; CYT,THY,URA
45 CM CT 1 0.15100 265265.6 ; 7,(1986),230; THY
46 CM HA 1 0.10800 307105.6 ; ged from 340. bsd on C6H6 nmodes; CYT,URA
47 CM H4 1 0.10800 307105.6 ; ged from 340. bsd on C6H6 nmodes; CYT,URA
48 CM H5 1 0.10800 307105.6 ; ged from 340. bsd on C6H6 nmodes; not assigned
49 CM N* 1 0.13650 374886.4 ; 7,(1986),230; CYT,THY,URA
50 CQ H5 1 0.10800 307105.6 ; ged from 340. bsd on C6H6 nmodes; ADE
51 CQ NC 1 0.13240 420073.6 ; 7,(1986),230; ADE
52 CT CT 1 0.15260 259408.0 ; 7,(1986),230; AA, SUGARS
53 CT HC 1 0.10900 284512.0 ; ged from 331 bsd on NMA nmodes; AA, SUGARS
54 CT H1 1 0.10900 284512.0 ; ged from 331 bsd on NMA nmodes; AA, RIBOSE
55 CT H2 1 0.10900 284512.0 ; ged from 331 bsd on NMA nmodes; SUGARS
56 CT H3 1 0.10900 284512.0 ; ged from 331 bsd on NMA nmodes; not assigned
57 CT HP 1 0.10900 284512.0 ; nged from 331; AA-lysine, methyl ammonium cation
58 CT N* 1 0.14750 282001.6 ; 7,(1986),230; ADE,CYT,GUA,THY,URA
59 CT N2 1 0.14630 282001.6 ; 7,(1986),230; ARG
60 CT OH 1 0.14100 267776.0 ; 7,(1986),230; SUGARS
61 CT OS 1 0.14100 267776.0 ; 7,(1986),230; NUCLEIC ACIDS
62 H N2 1 0.10100 363171.2 ; 7,(1986),230; ADE,CYT,GUA,ARG
63 H N* 1 0.10100 363171.2 ; plain unmethylated bases ADE,CYT,GUA,ARG
64 H NA 1 0.10100 363171.2 ; 7,(1986),230; GUA,URA,HIS
65 HO OH 1 0.09600 462750.4 ; 7,(1986),230; SUGARS,SER,TYR
66 HO OS 1 0.09600 462750.4 ; 7,(1986),230; NUCLEOTIDE ENDS
67 O2 P 1 0.14800 439320.0 ; 7,(1986),230; NA PHOSPHATES
68 OH P 1 0.16100 192464.0 ; 7,(1986),230; NA PHOSPHATES
69 OS P 1 0.16100 192464.0 ; 7,(1986),230; NA PHOSPHATES
70 C* HC 1 0.10800 307105.6 ; ged from 340. bsd on C6H6 nmodes, not needed AA
71 C N 1 0.13350 410032.0 ; 7,(1986),230; AA
72 C* CB 1 0.14590 324678.4 ; 7,(1986),230; TRP
73 C* CT 1 0.14950 265265.6 ; 7,(1986),230; TRP
74 C* CW 1 0.13520 456892.8 ; 7,(1986),230; TRP
75 CA CN 1 0.14000 392459.2 ; 7,(1986),230; TRP
76 CB CN 1 0.14190 374049.6 ; 7,(1986),230; TRP
77 CC CT 1 0.15040 265265.6 ; 7,(1986),230; HIS
78 CC CV 1 0.13750 428441.6 ; 7,(1986),230; HIS(delta)
79 CC CW 1 0.13710 433462.4 ; 7,(1986),230; HIS(epsilon)
80 CC NA 1 0.13850 353129.6 ; 7,(1986),230; HIS
81 CC NB 1 0.13940 343088.0 ; 7,(1986),230; HIS
82 CN NA 1 0.13800 358150.4 ; 7,(1986),230; TRP
83 CR H5 1 0.10800 307105.6 ; ged from 340. bsd on C6H6 nmodes;HIS
84 CR NA 1 0.13430 399153.6 ; 7,(1986),230; HIS
85 CR NB 1 0.13350 408358.4 ; 7,(1986),230; HIS
86 CT N 1 0.14490 282001.6 ; 7,(1986),230; AA
87 CT N3 1 0.14710 307105.6 ; 7,(1986),230; LYS
88 CT S 1 0.18100 189953.6 ; ged from 222.0 based on dimethylS nmodes
89 CT SH 1 0.18100 198321.6 ; ged from 222.0 based on methanethiol nmodes
90 CV H4 1 0.10800 307105.6 ; ged from 340. bsd on C6H6 nmodes; HIS
91 CV NB 1 0.13940 343088.0 ; 7,(1986),230; HIS
92 CW H4 1 0.10800 307105.6 ; ged from 340. bsd on C6H6 nmodes;HIS(epsilon,+)
93 CW NA 1 0.13810 357313.6 ; 7,(1986),230; HIS,TRP
94 H N 1 0.10100 363171.2 ; 7,(1986),230; AA
95 H N3 1 0.10100 363171.2 ; 7,(1986),230; LYS
96 HS SH 1 0.13360 229283.2 ; 7,(1986),230; CYS
97 S S 1 0.20380 138908.8 ; 7,(1986),230; CYX (SCHERAGA)
98 CT F 1 0.13800 307105.6 ; 13,(1992),963;CF4; R0=1.332 FOR CHF3
102 [ constrainttypes ]
103 ; this section is implemented manually from bond & angle values
105 ; constraints for rigid CH3 groups
106 MCH3 CT 2 0.166426
107 MCH3 S 2 0.193875
108 MCH3 MCH3 2 0.092163
109 ; constraints for rigid NH3 groups
110 MNH3 CT 2 0.158254
111 MNH3 MNH3 2 0.080229
113 ; angle-derived constraints for OH and SH groups in proteins
114 ; The constraint A-C is calculated from the angle A-B-C and bonds A-B, B-C.
115 C HO 2 0.195074
116 CA HO 2 0.195074
117 CT HO 2 0.194132
118 CT HS 2 0.235935
122 [ angletypes ]
123 ; i j k func th0 cth
124 HW OW HW 1 104.520 836.800 ; TIP3P water
125 HW HW OW 1 127.740 0.000 ; (found in crystallographic water with 3 bonds)
126 C C O 1 120.000 669.440 ; new99
127 C C OH 1 120.000 669.440 ; new99
128 CT C CT 1 117.000 527.184 ; new99
129 CT C OS 1 115.000 669.440 ; new99
130 O C OS 1 125.000 669.440 ; new99
131 H4 C C 1 120.000 418.400 ; new99
132 H4 C CM 1 115.000 418.400 ; new99
133 H4 C CT 1 115.000 418.400 ; new99
134 H4 C O 1 120.000 418.400 ; new99
135 H4 C OH 1 120.000 418.400 ; new99
136 H5 C N 1 120.000 418.400 ; new99
137 H5 C O 1 119.000 418.400 ; new99
138 H5 C OH 1 107.000 418.400 ; new99
139 H5 C OS 1 107.000 418.400 ; new99
140 CA CA OH 1 120.000 585.760 ; new99
141 CA OH HO 1 113.000 418.400 ; new99
142 F CA CA 1 121.000 585.760 ; new99
143 Cl CA CA 1 118.800 585.760 ; new99
144 Br CA CA 1 118.800 585.760 ; new99
145 I CA CA 1 118.800 585.760 ; new99
146 CM CM OS 1 125.000 669.440 ; new99
147 H4 CM OS 1 113.000 418.400 ; new99
148 HA CM HA 1 120.000 292.880 ; new99
149 HA CM CT 1 120.000 418.400 ; new99
150 H1 CT CM 1 109.500 418.400 ; new99
151 HC CT CM 1 109.500 418.400 ; new99
152 C CT OS 1 109.500 502.080 ; new99
153 CM CT CT 1 111.000 527.184 ; new99
154 CM CT OS 1 109.500 418.400 ; new99
155 CT CT CA 1 114.000 527.184 ; new99
156 OS CT OS 1 101.000 502.080 ; new99
157 F CT CT 1 109.000 418.400 ; new99
158 F CT H2 1 109.500 418.400 ; new99
159 Cl CT CT 1 108.500 418.400 ; new99
160 Cl CT H1 1 108.500 418.400 ; new99
161 Br CT CT 1 108.000 418.400 ; new99
162 Br CT H1 1 106.500 418.400 ; new99
163 I CT CT 1 106.000 418.400 ; new99
164 CB C NA 1 111.300 585.760 ; NA
165 CB C O 1 128.800 669.440 ;
166 CM C NA 1 114.100 585.760 ;
167 CM C O 1 125.300 669.440 ;
168 CT C O 1 120.400 669.440 ;
169 CT C O2 1 117.000 585.760 ;
170 CT C OH 1 110.000 669.440 ; new99
171 N* C NA 1 115.400 585.760 ;
172 N* C NC 1 118.600 585.760 ;
173 N* C O 1 120.900 669.440 ;
174 NA C O 1 120.600 669.440 ;
175 NC C O 1 122.500 669.440 ;
176 CT C N 1 116.600 585.760 ; AA general
177 N C O 1 122.900 669.440 ; AA general
178 O C O 1 126.000 669.440 ; AA COO- terminal residues
179 O2 C O2 1 126.000 669.440 ; AA GLU (SCH JPC 79,2379)
180 O C OH 1 120.000 669.440 ;
181 CA C CA 1 120.000 527.184 ; changed from 85.0 bsd on C6H6 nmodes; AA tyr
182 CA C OH 1 120.000 585.760 ; AA tyr
183 C CA CA 1 120.000 527.184 ; changed from 85.0 bsd on C6H6 nmodes
184 CA CA CA 1 120.000 527.184 ; changed from 85.0 bsd on C6H6 nmodes
185 CA CA CB 1 120.000 527.184 ; changed from 85.0 bsd on C6H6 nmodes
186 CA CA CT 1 120.000 585.760 ;
187 CA CA HA 1 120.000 418.400 ; new99
188 CA CA H4 1 120.000 418.400 ; new99
189 CB CA HA 1 120.000 418.400 ; new99
190 CB CA H4 1 120.000 418.400 ; new99
191 CB CA N2 1 123.500 585.760 ;
192 CB CA NC 1 117.300 585.760 ;
193 CM CA N2 1 120.100 585.760 ;
194 CM CA NC 1 121.500 585.760 ;
195 N2 CA NA 1 116.000 585.760 ;
196 N2 CA NC 1 119.300 585.760 ;
197 NA CA NC 1 123.300 585.760 ;
198 C CA HA 1 120.000 418.400 ; new99 tyr
199 N2 CA N2 1 120.000 585.760 ; AA arg
200 CN CA HA 1 120.000 418.400 ; new99 trp
201 CA CA CN 1 120.000 527.184 ; changed from 85.0 bsd on C6H6 nmodes; AA trp
202 C CB CB 1 119.200 527.184 ; changed from 85.0 bsd on C6H6 nmodes; NA gua
203 C CB NB 1 130.000 585.760 ;
204 CA CB CB 1 117.300 527.184 ; changed from 85.0 bsd on C6H6 nmodes; NA ade
205 CA CB NB 1 132.400 585.760 ;
206 CB CB N* 1 106.200 585.760 ;
207 CB CB NB 1 110.400 585.760 ;
208 CB CB NC 1 127.700 585.760 ;
209 N* CB NC 1 126.200 585.760 ;
210 C* CB CA 1 134.900 527.184 ; changed from 85.0 bsd on C6H6 nmodes; AA trp
211 C* CB CN 1 108.800 527.184 ; changed from 85.0 bsd on C6H6 nmodes; AA trp
212 CA CB CN 1 116.200 527.184 ; changed from 85.0 bsd on C6H6 nmodes; AA trp
213 H5 CK N* 1 123.050 418.400 ; new99
214 H5 CK NB 1 123.050 418.400 ; new99
215 N* CK NB 1 113.900 585.760 ;
216 C CM CM 1 120.700 527.184 ; changed from 85.0 bsd on C6H6 nmodes; NA thy
217 C CM CT 1 119.700 585.760 ;
218 C CM HA 1 119.700 418.400 ; new99
219 C CM H4 1 119.700 418.400 ; new99
220 CA CM CM 1 117.000 527.184 ; changed from 85.0 bsd on C6H6 nmodes; NA cyt
221 CA CM HA 1 123.300 418.400 ; new99
222 CA CM H4 1 123.300 418.400 ; new99
223 CM CM CT 1 119.700 585.760 ;
224 CM CM HA 1 119.700 418.400 ; new99
225 CM CM H4 1 119.700 418.400 ; new99
226 CM CM N* 1 121.200 585.760 ;
227 H4 CM N* 1 119.100 418.400 ; new99
228 H5 CQ NC 1 115.450 418.400 ; new99
229 NC CQ NC 1 129.100 585.760 ;
230 CM CT HC 1 109.500 418.400 ; changed based on NMA nmodes
231 CT CT CT 1 109.500 334.720 ;
232 CT CT HC 1 109.500 418.400 ; changed based on NMA nmodes
233 CT CT H1 1 109.500 418.400 ; changed based on NMA nmodes
234 CT CT H2 1 109.500 418.400 ; changed based on NMA nmodes
235 CT CT HP 1 109.500 418.400 ; changed based on NMA nmodes
236 CT CT N* 1 109.500 418.400 ;
237 CT CT OH 1 109.500 418.400 ;
238 CT CT OS 1 109.500 418.400 ;
239 HC CT HC 1 109.500 292.880 ;
240 H1 CT H1 1 109.500 292.880 ;
241 HP CT HP 1 109.500 292.880 ; AA lys, ch3nh4+
242 H2 CT N* 1 109.500 418.400 ; changed based on NMA nmodes
243 H1 CT N* 1 109.500 418.400 ; changed based on NMA nmodes
244 H1 CT OH 1 109.500 418.400 ; changed based on NMA nmodes
245 H1 CT OS 1 109.500 418.400 ; changed based on NMA nmodes
246 H2 CT OS 1 109.500 418.400 ; changed based on NMA nmodes
247 N* CT OS 1 109.500 418.400 ;
248 H1 CT N 1 109.500 418.400 ; AA general changed based on NMA nmodes
249 C CT H1 1 109.500 418.400 ; AA general changed based on NMA nmodes
250 C CT HP 1 109.500 418.400 ; AA zwitterion changed based on NMA nmodes
251 H1 CT S 1 109.500 418.400 ; AA cys changed based on NMA nmodes
252 H1 CT SH 1 109.500 418.400 ; AA cyx changed based on NMA nmodes
253 CT CT S 1 114.700 418.400 ; AA cyx (SCHERAGA JPC 79,1428)
254 CT CT SH 1 108.600 418.400 ; AA cys
255 H2 CT H2 1 109.500 292.880 ; AA lys
256 H1 CT N2 1 109.500 418.400 ; AA arg changed based on NMA nmodes
257 HP CT N3 1 109.500 418.400 ; AA lys, ch3nh3+, changed based on NMA nmodes
258 CA CT CT 1 114.000 527.184 ; AA phe tyr (SCH JPC 79,2379)
259 C CT HC 1 109.500 418.400 ; AA gln changed based on NMA nmodes
260 C CT N 1 110.100 527.184 ; AA general
261 CT CT N2 1 111.200 669.440 ; AA arg (JCP 76, 1439)
262 CT CT N 1 109.700 669.440 ; AA ala, general (JACS 94, 2657)
263 C CT CT 1 111.100 527.184 ; AA general
264 CA CT HC 1 109.500 418.400 ; AA tyr changed based on NMA nmodes
265 CT CT N3 1 111.200 669.440 ; AA lys (JCP 76, 1439)
266 CC CT CT 1 113.100 527.184 ; AA his
267 CC CT HC 1 109.500 418.400 ; AA his changed based on NMA nmodes
268 C CT N3 1 111.200 669.440 ; AA amino terminal residues
269 C* CT CT 1 115.600 527.184 ; AA trp
270 C* CT HC 1 109.500 418.400 ; AA trp changed based on NMA nmodes
271 CT CC NA 1 120.000 585.760 ; AA his
272 CT CC CV 1 120.000 585.760 ; AA his
273 CT CC NB 1 120.000 585.760 ; AA his
274 CV CC NA 1 120.000 585.760 ; AA his
275 CW CC NA 1 120.000 585.760 ; AA his
276 CW CC NB 1 120.000 585.760 ; AA his
277 CT CC CW 1 120.000 585.760 ; AA his
278 H5 CR NA 1 120.000 418.400 ; new99 his
279 H5 CR NB 1 120.000 418.400 ; new99 his
280 NA CR NA 1 120.000 585.760 ; AA his
281 NA CR NB 1 120.000 585.760 ; AA his
282 CC CV H4 1 120.000 418.400 ; new99 his
283 CC CV NB 1 120.000 585.760 ; AA his
284 H4 CV NB 1 120.000 418.400 ; new99 his
285 CC CW H4 1 120.000 418.400 ; new99 his
286 CC CW NA 1 120.000 585.760 ; AA his
287 H4 CW NA 1 120.000 418.400 ; new99 his
288 C* CW H4 1 120.000 418.400 ; new99 trp
289 C* CW NA 1 108.700 585.760 ; AA trp
290 CT C* CW 1 125.000 585.760 ; AA trp
291 CB C* CT 1 128.600 585.760 ; AA trp
292 CB C* CW 1 106.400 527.184 ; changed from 85.0 bsd on C6H6 nmodes; AA trp
293 CA CN NA 1 132.800 585.760 ; AA trp
294 CB CN NA 1 104.400 585.760 ; AA trp
295 CA CN CB 1 122.700 527.184 ; changed from 85.0 bsd on C6H6 nmodes; AA trp
296 C N CT 1 121.900 418.400 ; AA general
297 C N H 1 120.000 418.400 ; new99 general, gln, asn,changed based on NMA nmodes
298 CT N H 1 118.040 418.400 ; new99 general, changed based on NMA nmodes
299 CT N CT 1 118.000 418.400 ; AA pro (DETAR JACS 99,1232)
300 H N H 1 120.000 292.880 ; ade,cyt,gua,gln,asn **
301 C N* CM 1 121.600 585.760 ;
302 C N* CT 1 117.600 585.760 ;
303 C N* H 1 119.200 418.400 ; new99
304 CB N* CK 1 105.400 585.760 ;
305 CB N* CT 1 125.800 585.760 ;
306 CB N* H 1 125.800 418.400 ; new99
307 CK N* CT 1 128.800 585.760 ;
308 CK N* H 1 128.800 418.400 ; new99 for unmethylated n.a. bases,chngd bsd NMA nmodes
309 CM N* CT 1 121.200 585.760 ;
310 CM N* H 1 121.200 418.400 ; new99 for unmethylated n.a. bases,chngd bsd NMA nmodes
311 CA N2 H 1 120.000 418.400 ; new99
312 H N2 H 1 120.000 292.880 ;
313 CT N2 H 1 118.400 418.400 ; new99 arg
314 CA N2 CT 1 123.200 418.400 ; AA arg
315 CT N3 H 1 109.500 418.400 ; AA lys, changed based on NMA nmodes
316 CT N3 CT 1 109.500 418.400 ; AA pro/nt
317 H N3 H 1 109.500 292.880 ; AA lys, AA(end)
318 C NA C 1 126.400 585.760 ;
319 C NA CA 1 125.200 585.760 ;
320 C NA H 1 116.800 418.400 ; new99
321 CA NA H 1 118.000 418.400 ; new99
322 CC NA CR 1 120.000 585.760 ; AA his
323 CC NA H 1 120.000 418.400 ; new99 his
324 CR NA CW 1 120.000 585.760 ; AA his
325 CR NA H 1 120.000 418.400 ; new99 his
326 CW NA H 1 120.000 418.400 ; new99 his
327 CN NA CW 1 111.600 585.760 ; AA trp
328 CN NA H 1 123.100 418.400 ; new99 trp
329 CB NB CK 1 103.800 585.760 ;
330 CC NB CR 1 117.000 585.760 ; AA his
331 CR NB CV 1 117.000 585.760 ; AA his
332 C NC CA 1 120.500 585.760 ;
333 CA NC CB 1 112.200 585.760 ;
334 CA NC CQ 1 118.600 585.760 ;
335 CB NC CQ 1 111.000 585.760 ;
336 C OH HO 1 113.000 418.400 ; new99
337 CT OH HO 1 108.500 460.240 ;
338 HO OH P 1 108.500 376.560 ;
339 CT OS CT 1 109.500 502.080 ;
340 CT OS P 1 120.500 836.800 ;
341 P OS P 1 120.500 836.800 ;
342 O2 P OH 1 108.230 376.560 ;
343 O2 P O2 1 119.900 1171.520 ;
344 O2 P OS 1 108.230 836.800 ;
345 OH P OS 1 102.600 376.560 ;
346 OS P OS 1 102.600 376.560 ;
347 CT S CT 1 98.900 518.816 ; AA met
348 CT S S 1 103.700 569.024 ; AA cyx (SCHERAGA JPC 79,1428)
349 CT SH HS 1 96.000 359.824 ; changed from 44.0 based on methanethiol nmodes
350 HS SH HS 1 92.070 292.880 ; AA cys
351 F CT F 1 109.100 644.336 ; JCC,13,(1992),963;
352 F CT H1 1 109.500 418.400 ; new99
353 N C N 1 120.000 585.760 ; Added for Urea (same as N2-CA-N2) - EJS
355 [ dihedraltypes ]
356 ;i j k l func phase kd pn
357 CA CA CA OH 4 180.00 4.60240 2 ; new99
358 H5 O C OH 4 180.00 4.60240 2 ; new99
359 H5 O C OS 4 180.00 4.60240 2 ; new99
360 CM CT CM HA 4 180.00 4.60240 2 ; new99
361 CA CA CA Br 4 180.00 4.60240 2 ; new99
362 CM H4 C O 4 180.00 4.60240 2 ; new99
363 C CT N H 4 180.00 4.60240 2 ; new99
364 C CT N O 4 180.00 4.60240 2 ; new99
365 CB CK N* CT 4 180.00 4.18400 2 ;
366 CK CB N* CT 4 180.00 4.18400 2 ;
367 C CM N* CT 4 180.00 4.18400 2 ; dac guess, 9/94
368 CT N* C CM 4 180.00 4.18400 2 ;
369 CM C CM CT 4 180.00 4.60240 2 ;
370 CT O C OH 4 180.00 43.93200 2 ;
371 NA CV CC CT 4 180.00 4.60240 2 ;
372 NB CW CC CT 4 180.00 4.60240 2 ;
373 NA CW CC CT 4 180.00 4.60240 2 ;
374 CW CB C* CT 4 180.00 4.60240 2 ;
375 CA CA CA CT 4 180.00 4.60240 2 ;
376 C CM CM CT 4 180.00 4.60240 2 ; dac guess, 9/94
377 NC CM CA N2 4 180.00 4.60240 2 ; dac guess, 9/94
378 CB NC CA N2 4 180.00 4.60240 2 ; dac, 10/94
379 NA NC CA N2 4 180.00 4.60240 2 ; dac, 10/94
380 CA CA C OH 4 180.00 4.60240 2 ;
381 CT CV CC NA 4 180.00 4.60240 2 ;
382 CT CW CC NB 4 180.00 4.60240 2 ;
383 CT CW CC NA 4 180.00 4.60240 2 ;
384 CB CT C* CW 4 180.00 4.60240 2 ;
385 CM N2 CA NC 4 180.00 4.60240 2 ;
386 CB N2 CA NC 4 180.00 4.60240 2 ;
387 N2 NA CA NC 4 180.00 4.60240 2 ;
388 N N C O 4 180.00 43.93200 2 ; urea
389 X O2 C O2 4 180.00 43.93200 2 ; JCC,7,(1986),230
390 X N2 CA N2 4 180.00 43.93200 2 ; JCC,7,(1986),230
391 X CT N CT 4 180.00 4.18400 2 ; JCC,7,(1986),230
392 X X C O 4 180.00 43.93200 2 ; JCC,7,(1986),230
393 X X N H 4 180.00 4.18400 2 ; JCC,7,(1986),230
394 X X N2 H 4 180.00 4.18400 2 ; JCC,7,(1986),230
395 X X NA H 4 180.00 4.18400 2 ; JCC,7,(1986),230
396 X X CA HA 4 180.00 4.60240 2 ; bsd.on C6H6 nmodes
397 X X CW H4 4 180.00 4.60240 2 ;
398 X X CR H5 4 180.00 4.60240 2 ;
399 X X CV H4 4 180.00 4.60240 2 ;
400 X X CQ H5 4 180.00 4.60240 2 ;
401 X X CK H5 4 180.00 4.60240 2 ;
402 X X CM H4 4 180.00 4.60240 2 ;
403 X X CM HA 4 180.00 4.60240 2 ;
404 X X CA H4 4 180.00 4.60240 2 ; bsd.on C6H6 nmodes
405 X X CA H5 4 180.00 4.60240 2 ; bsd.on C6H6 nmodes
408 [ dihedraltypes ]
409 ;i j k l func
410 CT CT OS CT 9 0.0 1.60247 3 ;
411 CT CT OS CT 9 180.0 0.41840 2 ;
412 C N CT C 9 0.0 1.12968 2 ; new for 99sb
413 C N CT C 9 0.0 1.75728 3 ; new for 99sb
414 N CT C N 9 180.0 1.88280 1 ; new for 99sb
415 N CT C N 9 180.0 6.61072 2 ; new for 99sb
416 N CT C N 9 180.0 2.30120 3 ; new for 99sb
417 CT CT N C 9 0.0 8.36800 1 ; new for 99sb
418 CT CT N C 9 0.0 8.36800 2 ; new for 99sb
419 CT CT N C 9 0.0 1.67360 3 ; new for 99sb
420 CT CT C N 9 0.0 0.83680 1 ; new for 99sb
421 CT CT C N 9 0.0 0.83680 2 ; new for 99sb
422 CT CT C N 9 0.0 1.67360 3 ; new for 99sb
423 H N C O 9 180.0 10.46000 2 ; JCC,7,(1986),230
424 H N C O 9 0.0 8.36800 1 ; J.C.cistrans-NMA DE
425 CT S S CT 9 0.0 14.64400 2 ; JCC,7,(1986),230
426 CT S S CT 9 0.0 2.51040 3 ; JCC,7,(1986),230
427 OS CT CT OS 9 0.0 0.60250 3 ; parm98, TC,PC,PAK
428 OS CT CT OS 9 0.0 4.91620 2 ; Piotr et al.
429 OS CT CT OH 9 0.0 0.60250 3 ; parm98, TC,PC,PAK
430 OS CT CT OH 9 0.0 4.91620 2 ; parm98, TC,PC,PAK
431 OH CT CT OH 9 0.0 0.60250 3 ; parm98, TC,PC,PAK
432 OH CT CT OH 9 0.0 4.91620 2 ; parm98, TC,PC,PAK
433 OH P OS CT 9 0.0 1.04600 3 ; JCC,7,(1986),230
434 OH P OS CT 9 0.0 5.02080 2 ; gg> ene.631g*/mp2
435 OS P OS CT 9 0.0 1.04600 3 ; JCC,7,(1986),230
436 OS P OS CT 9 0.0 5.02080 2 ; gg> ene.631g*/mp2
437 OS CT N* CK 9 0.0 10.46000 1 ; parm98, TC,PC,PAK
438 OS CT N* CM 9 0.0 10.46000 1 ; parm98, TC,PC,PAK
439 H1 CT C O 9 0.0 3.34720 1 ; Junmei et al, 1999
440 H1 CT C O 9 180.0 0.33472 3 ; Junmei et al, 1999
441 HC CT C O 9 0.0 3.34720 1 ; Junmei et al, 1999
442 HC CT C O 9 180.0 0.33472 3 ; Junmei et al, 1999
443 HC CT CT HC 9 0.0 0.62760 3 ; Junmei et al, 1999
444 HC CT CT CT 9 0.0 0.66944 3 ; Junmei et al, 1999
445 HC CT CM CM 9 180.0 1.58992 3 ; Junmei et al, 1999
446 HC CT CM CM 9 0.0 4.81160 1 ; Junmei et al, 1999
447 HO OH CT CT 9 0.0 0.66944 3 ; Junmei et al, 1999
448 HO OH CT CT 9 0.0 1.04600 1 ; Junmei et al, 1999
449 HO OH C O 9 180.0 9.62320 2 ; Junmei et al, 1999
450 HO OH C O 9 0.0 7.94960 1 ; Junmei et al, 1999
451 CM CM C O 9 180.0 9.10020 2 ; Junmei et al, 1999
452 CM CM C O 9 0.0 1.25520 3 ; Junmei et al, 1999
453 CT CM CM CT 9 180.0 27.82360 2 ; Junmei et al, 1999
454 CT CM CM CT 9 180.0 7.94960 1 ; Junmei et al, 1999
455 CT CT CT CT 9 0.0 0.75312 3 ; Junmei et al, 1999
456 CT CT CT CT 9 180.0 1.04600 2 ; Junmei et al, 1999
457 CT CT CT CT 9 180.0 0.83680 1 ; Junmei et al, 1999
458 CT CT OS C 9 0.0 1.60247 3 ; Junmei et al, 1999
459 CT CT OS C 9 180.0 3.34720 1 ; Junmei et al, 1999
460 CT OS CT OS 9 0.0 0.41840 3 ; Junmei et al, 1999
461 CT OS CT OS 9 180.0 3.55640 2 ; Junmei et al, 1999
462 CT OS CT OS 9 180.0 5.64840 1 ; Junmei et al, 1999
463 O C OS CT 9 180.0 11.29680 2 ; Junmei et al, 1999
464 O C OS CT 9 180.0 5.85760 1 ; Junmei et al, 1999
465 F CT CT F 9 180.0 5.02080 1 ; Junmei et al, 1999
466 Cl CT CT Cl 9 180.0 1.88280 1 ; Junmei et al, 1999
467 Br CT CT Br 9 0.0 0.00000 0 ; Junmei et al, 1999
468 H1 CT CT OS 9 0.0 1.04600 1 ; Junmei et al, 1999
469 H1 CT CT OH 9 0.0 1.04600 1 ; Junmei et al, 1999
470 H1 CT CT F 9 0.0 0.79496 1 ; Junmei et al, 1999
471 H1 CT CT Cl 9 0.0 1.04600 1 ; Junmei et al, 1999
472 H1 CT CT Br 9 0.0 2.30120 1 ; Junmei et al, 1999
473 HC CT CT OS 9 0.0 1.04600 1 ; Junmei et al, 1999
474 HC CT CT OH 9 0.0 1.04600 1 ; Junmei et al, 1999
475 HC CT CT F 9 0.0 0.79496 1 ; Junmei et al, 1999
476 HC CT CT Cl 9 0.0 1.04600 1 ; Junmei et al, 1999
477 HC CT CT Br 9 0.0 2.30120 1 ; Junmei et al, 1999
478 CT OS CT N* 9 0.0 1.60247 3 ; parm98.dat, TC,PC,PAK
479 CT OS CT N* 9 0.0 2.71960 2 ; Piotr et al.
480 X C C X 9 180.0 15.16700 2 ; Junmei et al, 1999
481 X C O X 9 180.0 11.71520 2 ; Junmei et al, 1999
482 X C OS X 9 180.0 11.29680 2 ; Junmei et al, 1999
483 X CA OH X 9 180.0 3.76560 2 ; Junmei et al, 99
484 X CM OS X 9 180.0 4.39320 2 ; Junmei et al, 1999
485 X C CA X 9 180.0 15.16700 2 ; intrpol.bsd.on C6H6
486 X C CB X 9 180.0 12.55200 2 ; intrpol.bsd.on C6H6
487 X C CM X 9 180.0 9.10020 2 ; intrpol.bsd.on C6H6
488 X C N* X 9 180.0 6.06680 2 ; JCC,7,(1986),230
489 X C NA X 9 180.0 5.64840 2 ; JCC,7,(1986),230
490 X C NC X 9 180.0 16.73600 2 ; JCC,7,(1986),230
491 X C OH X 9 180.0 9.62320 2 ; Junmei et al, 1999
492 X C CT X 9 0.0 0.00000 0 ; JCC,7,(1986),230
493 X CA CA X 9 180.0 15.16700 2 ; intrpol.bsd.on C6H6
494 X CA CB X 9 180.0 14.64400 2 ; intrpol.bsd.on C6H6
495 X CA CM X 9 180.0 10.66920 2 ; intrpol.bsd.on C6H6
496 X CA CT X 9 0.0 0.00000 0 ; JCC,7,(1986),230
497 X CA N2 X 9 180.0 10.04160 2 ; reinterpolated 93'
498 X CA NA X 9 180.0 6.27600 2 ; JCC,7,(1986),230
499 X CA NC X 9 180.0 20.08320 2 ; JCC,7,(1986),230
500 X CB CB X 9 180.0 22.80280 2 ; intrpol.bsd.on C6H6
501 X CB N* X 9 180.0 6.90360 2 ; JCC,7,(1986),230
502 X CB NB X 9 180.0 10.66920 2 ; JCC,7,(1986),230
503 X CB NC X 9 180.0 17.36360 2 ; JCC,7,(1986),230
504 X CK N* X 9 180.0 7.11280 2 ; JCC,7,(1986),230
505 X CK NB X 9 180.0 41.84000 2 ; JCC,7,(1986),230
506 X CM CM X 9 180.0 27.82360 2 ; intrpol.bsd.on C6H6
507 X CM CT X 9 0.0 0.00000 0 ; JCC,7,(1986),230
508 X CM N* X 9 180.0 7.74040 2 ; JCC,7,(1986),230
509 X CQ NC X 9 180.0 28.45120 2 ; JCC,7,(1986),230
510 X CT CT X 9 0.0 0.65084 3 ; JCC,7,(1986),230
511 X CT N X 9 0.0 0.00000 0 ; JCC,7,(1986),230
512 X CT N* X 9 0.0 0.00000 0 ; JCC,7,(1986),230
513 X CT N2 X 9 0.0 0.00000 0 ; JCC,7,(1986),230
514 X CT OH X 9 0.0 0.69733 3 ; JCC,7,(1986),230
515 X CT OS X 9 0.0 1.60387 3 ; JCC,7,(1986),230
516 X OH P X 9 0.0 1.04600 3 ; JCC,7,(1986),230
517 X OS P X 9 0.0 1.04600 3 ; JCC,7,(1986),230
518 X C N X 9 180.0 10.46000 2 ; AA,NMA
519 X CT N3 X 9 0.0 0.65084 3 ; JCC,7,(1986),230
520 X CT S X 9 0.0 1.39467 3 ; JCC,7,(1986),230
521 X CT SH X 9 0.0 1.04600 3 ; JCC,7,(1986),230
522 X C* CB X 9 180.0 7.00820 2 ; intrpol.bsd.onC6H6aa
523 X C* CT X 9 0.0 0.00000 0 ; JCC,7,(1986),230
524 X C* CW X 9 180.0 27.30060 2 ; intrpol.bsd.on C6H6
525 X CA CN X 9 180.0 15.16700 2 ; reinterpolated 93'
526 X CB CN X 9 180.0 12.55200 2 ; reinterpolated 93'
527 X CC CT X 9 0.0 0.00000 0 ; JCC,7,(1986),230
528 X CC CV X 9 180.0 21.54760 2 ; intrpol.bsd.on C6H6
529 X CC CW X 9 180.0 22.48900 2 ; intrpol.bsd.on C6H6
530 X CC NA X 9 180.0 5.85760 2 ; JCC,7,(1986),230
531 X CC NB X 9 180.0 10.04160 2 ; JCC,7,(1986),230
532 X CN NA X 9 180.0 6.38060 2 ; reinterpolated 93'
533 X CR NA X 9 180.0 9.72780 2 ; JCC,7,(1986),230
534 X CR NB X 9 180.0 20.92000 2 ; JCC,7,(1986),230
535 X CV NB X 9 180.0 10.04160 2 ; JCC,7,(1986),230
536 X CW NA X 9 180.0 6.27600 2 ; JCC,7,(1986),230
538 ; Modified amino acid torsions in Amber99SB-ILDN
539 ; These should not override the general torsion for the atom types,
540 ; so to avoid introducing extra new atom types we list them explicitly for
541 ; the residues in question:
543 #define torsion_ILE_N_CA_CB_CG2_mult1 0.0 0.8158800 1 ; Proteins 78, 1950 (2010)
544 #define torsion_ILE_N_CA_CB_CG2_mult2 0.0 -3.5396640 2 ; Proteins 78, 1950 (2010)
546 #define torsion_LEU_C_CA_CB_CG_mult1 0.0 2.3890640 1 ; Proteins 78, 1950 (2010)
547 #define torsion_LEU_C_CA_CB_CG_mult2 0.0 -1.4978720 2 ; Proteins 78, 1950 (2010)
548 #define torsion_LEU_C_CA_CB_CG_mult3 0.0 0.5648400 3 ; Proteins 78, 1950 (2010)
550 #define torsion_ASP_N_CA_CB_CG_mult1 0.0 -11.024840 1 ; Proteins 78, 1950 (2010)
551 #define torsion_ASP_N_CA_CB_CG_mult2 0.0 -4.978960 2 ; Proteins 78, 1950 (2010)
552 #define torsion_ASP_N_CA_CB_CG_mult3 0.0 -0.029288 3 ; Proteins 78, 1950 (2010)
553 #define torsion_ASP_N_CA_CB_CG_mult4 0.0 1.769832 4 ; Proteins 78, 1950 (2010)
554 #define torsion_ASP_N_CA_CB_CG_mult5 0.0 0.970688 5 ; Proteins 78, 1950 (2010)
555 #define torsion_ASP_N_CA_CB_CG_mult6 0.0 -0.891192 6 ; Proteins 78, 1950 (2010)
557 #define torsion_ASP_CA_CB_CG_OD_mult1 0.0 0.0 1 ; Proteins 78, 1950 (2010)
558 #define torsion_ASP_CA_CB_CG_OD_mult2 0.0 -1.853512 2 ; Proteins 78, 1950 (2010)
559 #define torsion_ASP_CA_CB_CG_OD_mult3 0.0 0.0 3 ; Proteins 78, 1950 (2010)
560 #define torsion_ASP_CA_CB_CG_OD_mult4 0.0 -0.577392 4 ; Proteins 78, 1950 (2010)
561 #define torsion_ASP_CA_CB_CG_OD_mult5 0.0 0.0 5 ; Proteins 78, 1950 (2010)
562 #define torsion_ASP_CA_CB_CG_OD_mult6 0.0 -0.054392 6 ; Proteins 78, 1950 (2010)
564 #define torsion_ASN_C_CA_CB_CG_mult1 0.0 2.389064 1 ; Proteins 78, 1950 (2010)
565 #define torsion_ASN_C_CA_CB_CG_mult2 0.0 -2.493664 2 ; Proteins 78, 1950 (2010)
566 #define torsion_ASN_C_CA_CB_CG_mult3 0.0 0.493712 3 ; Proteins 78, 1950 (2010)
567 #define torsion_ASN_C_CA_CB_CG_mult4 0.0 -1.744728 4 ; Proteins 78, 1950 (2010)
568 #define torsion_ASN_C_CA_CB_CG_mult5 0.0 0.435136 5 ; Proteins 78, 1950 (2010)
569 #define torsion_ASN_C_CA_CB_CG_mult6 0.0 -0.422584 6 ; Proteins 78, 1950 (2010)
571 #define torsion_ASN_CA_CB_CG_ND2_mult1 0.0 -4.376464 1 ; Proteins 78, 1950 (2010)
572 #define torsion_ASN_CA_CB_CG_ND2_mult2 0.0 -0.757304 2 ; Proteins 78, 1950 (2010)
573 #define torsion_ASN_CA_CB_CG_ND2_mult3 0.0 -0.146440 3 ; Proteins 78, 1950 (2010)
574 #define torsion_ASN_CA_CB_CG_ND2_mult4 0.0 0.418400 4 ; Proteins 78, 1950 (2010)
575 #define torsion_ASN_CA_CB_CG_ND2_mult5 0.0 0.543920 5 ; Proteins 78, 1950 (2010)
576 #define torsion_ASN_CA_CB_CG_ND2_mult6 0.0 -0.443504 6 ; Proteins 78, 1950 (2010)