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
100 ; New atomtype for C5' in DNA/RNA (checked with conversion and is the same as CT)
102 CI H1 1 0.10900 284512.0
103 CI CT 1 0.15260 259408.0
104 CI OH 1 0.14100 267776.0
105 CI OS 1 0.14100 267776.0
109 ; this section is implemented manually from bond & angle values
111 ; constraints for rigid CH3 groups
115 ; constraints for rigid NH3 groups
119 ; angle-derived constraints for OH and SH groups in proteins
120 ; The constraint A-C is calculated from the angle A-B-C and bonds A-B, B-C.
130 HW OW HW 1 104.520 836.800 ; TIP3P water
131 HW HW OW 1 127.740 0.000 ; (found in crystallographic water with 3 bonds)
132 C C O 1 120.000 669.440 ; new99
133 C C OH 1 120.000 669.440 ; new99
134 CT C CT 1 117.000 527.184 ; new99
135 CT C OS 1 115.000 669.440 ; new99
136 O C OS 1 125.000 669.440 ; new99
137 H4 C C 1 120.000 418.400 ; new99
138 H4 C CM 1 115.000 418.400 ; new99
139 H4 C CT 1 115.000 418.400 ; new99
140 H4 C O 1 120.000 418.400 ; new99
141 H4 C OH 1 120.000 418.400 ; new99
142 H5 C N 1 120.000 418.400 ; new99
143 H5 C O 1 119.000 418.400 ; new99
144 H5 C OH 1 107.000 418.400 ; new99
145 H5 C OS 1 107.000 418.400 ; new99
146 CA CA OH 1 120.000 585.760 ; new99
147 CA OH HO 1 113.000 418.400 ; new99
148 F CA CA 1 121.000 585.760 ; new99
149 Cl CA CA 1 118.800 585.760 ; new99
150 Br CA CA 1 118.800 585.760 ; new99
151 I CA CA 1 118.800 585.760 ; new99
152 CM CM OS 1 125.000 669.440 ; new99
153 H4 CM OS 1 113.000 418.400 ; new99
154 HA CM HA 1 120.000 292.880 ; new99
155 HA CM CT 1 120.000 418.400 ; new99
156 H1 CT CM 1 109.500 418.400 ; new99
157 HC CT CM 1 109.500 418.400 ; new99
158 C CT OS 1 109.500 502.080 ; new99
159 CM CT CT 1 111.000 527.184 ; new99
160 CM CT OS 1 109.500 418.400 ; new99
161 CT CT CA 1 114.000 527.184 ; new99
162 OS CT OS 1 101.000 502.080 ; new99
163 F CT CT 1 109.000 418.400 ; new99
164 F CT H2 1 109.500 418.400 ; new99
165 Cl CT CT 1 108.500 418.400 ; new99
166 Cl CT H1 1 108.500 418.400 ; new99
167 Br CT CT 1 108.000 418.400 ; new99
168 Br CT H1 1 106.500 418.400 ; new99
169 I CT CT 1 106.000 418.400 ; new99
170 CB C NA 1 111.300 585.760 ; NA
171 CB C O 1 128.800 669.440 ;
172 CM C NA 1 114.100 585.760 ;
173 CM C O 1 125.300 669.440 ;
174 CT C O 1 120.400 669.440 ;
175 CT C O2 1 117.000 585.760 ;
176 CT C OH 1 110.000 669.440 ; new99
177 N* C NA 1 115.400 585.760 ;
178 N* C NC 1 118.600 585.760 ;
179 N* C O 1 120.900 669.440 ;
180 NA C O 1 120.600 669.440 ;
181 NC C O 1 122.500 669.440 ;
182 CT C N 1 116.600 585.760 ; AA general
183 N C O 1 122.900 669.440 ; AA general
184 O C O 1 126.000 669.440 ; AA COO- terminal residues
185 O2 C O2 1 126.000 669.440 ; AA GLU (SCH JPC 79,2379)
186 O C OH 1 120.000 669.440 ;
187 CA C CA 1 120.000 527.184 ; changed from 85.0 bsd on C6H6 nmodes; AA tyr
188 CA C OH 1 120.000 585.760 ; AA tyr
189 C CA CA 1 120.000 527.184 ; changed from 85.0 bsd on C6H6 nmodes
190 CA CA CA 1 120.000 527.184 ; changed from 85.0 bsd on C6H6 nmodes
191 CA CA CB 1 120.000 527.184 ; changed from 85.0 bsd on C6H6 nmodes
192 CA CA CT 1 120.000 585.760 ;
193 CA CA HA 1 120.000 418.400 ; new99
194 CA CA H4 1 120.000 418.400 ; new99
195 CB CA HA 1 120.000 418.400 ; new99
196 CB CA H4 1 120.000 418.400 ; new99
197 CB CA N2 1 123.500 585.760 ;
198 CB CA NC 1 117.300 585.760 ;
199 CM CA N2 1 120.100 585.760 ;
200 CM CA NC 1 121.500 585.760 ;
201 N2 CA NA 1 116.000 585.760 ;
202 N2 CA NC 1 119.300 585.760 ;
203 NA CA NC 1 123.300 585.760 ;
204 C CA HA 1 120.000 418.400 ; new99 tyr
205 N2 CA N2 1 120.000 585.760 ; AA arg
206 CN CA HA 1 120.000 418.400 ; new99 trp
207 CA CA CN 1 120.000 527.184 ; changed from 85.0 bsd on C6H6 nmodes; AA trp
208 C CB CB 1 119.200 527.184 ; changed from 85.0 bsd on C6H6 nmodes; NA gua
209 C CB NB 1 130.000 585.760 ;
210 CA CB CB 1 117.300 527.184 ; changed from 85.0 bsd on C6H6 nmodes; NA ade
211 CA CB NB 1 132.400 585.760 ;
212 CB CB N* 1 106.200 585.760 ;
213 CB CB NB 1 110.400 585.760 ;
214 CB CB NC 1 127.700 585.760 ;
215 N* CB NC 1 126.200 585.760 ;
216 C* CB CA 1 134.900 527.184 ; changed from 85.0 bsd on C6H6 nmodes; AA trp
217 C* CB CN 1 108.800 527.184 ; changed from 85.0 bsd on C6H6 nmodes; AA trp
218 CA CB CN 1 116.200 527.184 ; changed from 85.0 bsd on C6H6 nmodes; AA trp
219 H5 CK N* 1 123.050 418.400 ; new99
220 H5 CK NB 1 123.050 418.400 ; new99
221 N* CK NB 1 113.900 585.760 ;
222 C CM CM 1 120.700 527.184 ; changed from 85.0 bsd on C6H6 nmodes; NA thy
223 C CM CT 1 119.700 585.760 ;
224 C CM HA 1 119.700 418.400 ; new99
225 C CM H4 1 119.700 418.400 ; new99
226 CA CM CM 1 117.000 527.184 ; changed from 85.0 bsd on C6H6 nmodes; NA cyt
227 CA CM HA 1 123.300 418.400 ; new99
228 CA CM H4 1 123.300 418.400 ; new99
229 CM CM CT 1 119.700 585.760 ;
230 CM CM HA 1 119.700 418.400 ; new99
231 CM CM H4 1 119.700 418.400 ; new99
232 CM CM N* 1 121.200 585.760 ;
233 H4 CM N* 1 119.100 418.400 ; new99
234 H5 CQ NC 1 115.450 418.400 ; new99
235 NC CQ NC 1 129.100 585.760 ;
236 CM CT HC 1 109.500 418.400 ; changed based on NMA nmodes
237 CT CT CT 1 109.500 334.720 ;
238 CT CT HC 1 109.500 418.400 ; changed based on NMA nmodes
239 CT CT H1 1 109.500 418.400 ; changed based on NMA nmodes
240 CT CT H2 1 109.500 418.400 ; changed based on NMA nmodes
241 CT CT HP 1 109.500 418.400 ; changed based on NMA nmodes
242 CT CT N* 1 109.500 418.400 ;
243 CT CT OH 1 109.500 418.400 ;
244 CT CT OS 1 109.500 418.400 ;
245 HC CT HC 1 109.500 292.880 ;
246 H1 CT H1 1 109.500 292.880 ;
247 HP CT HP 1 109.500 292.880 ; AA lys, ch3nh4+
248 H2 CT N* 1 109.500 418.400 ; changed based on NMA nmodes
249 H1 CT N* 1 109.500 418.400 ; changed based on NMA nmodes
250 H1 CT OH 1 109.500 418.400 ; changed based on NMA nmodes
251 H1 CT OS 1 109.500 418.400 ; changed based on NMA nmodes
252 H2 CT OS 1 109.500 418.400 ; changed based on NMA nmodes
253 N* CT OS 1 109.500 418.400 ;
254 H1 CT N 1 109.500 418.400 ; AA general changed based on NMA nmodes
255 C CT H1 1 109.500 418.400 ; AA general changed based on NMA nmodes
256 C CT HP 1 109.500 418.400 ; AA zwitterion changed based on NMA nmodes
257 H1 CT S 1 109.500 418.400 ; AA cys changed based on NMA nmodes
258 H1 CT SH 1 109.500 418.400 ; AA cyx changed based on NMA nmodes
259 CT CT S 1 114.700 418.400 ; AA cyx (SCHERAGA JPC 79,1428)
260 CT CT SH 1 108.600 418.400 ; AA cys
261 H2 CT H2 1 109.500 292.880 ; AA lys
262 H1 CT N2 1 109.500 418.400 ; AA arg changed based on NMA nmodes
263 HP CT N3 1 109.500 418.400 ; AA lys, ch3nh3+, changed based on NMA nmodes
264 CA CT CT 1 114.000 527.184 ; AA phe tyr (SCH JPC 79,2379)
265 C CT HC 1 109.500 418.400 ; AA gln changed based on NMA nmodes
266 C CT N 1 110.100 527.184 ; AA general
267 CT CT N2 1 111.200 669.440 ; AA arg (JCP 76, 1439)
268 CT CT N 1 109.700 669.440 ; AA ala, general (JACS 94, 2657)
269 C CT CT 1 111.100 527.184 ; AA general
270 CA CT HC 1 109.500 418.400 ; AA tyr changed based on NMA nmodes
271 CT CT N3 1 111.200 669.440 ; AA lys (JCP 76, 1439)
272 CC CT CT 1 113.100 527.184 ; AA his
273 CC CT HC 1 109.500 418.400 ; AA his changed based on NMA nmodes
274 C CT N3 1 111.200 669.440 ; AA amino terminal residues
275 C* CT CT 1 115.600 527.184 ; AA trp
276 C* CT HC 1 109.500 418.400 ; AA trp changed based on NMA nmodes
277 CT CC NA 1 120.000 585.760 ; AA his
278 CT CC CV 1 120.000 585.760 ; AA his
279 CT CC NB 1 120.000 585.760 ; AA his
280 CV CC NA 1 120.000 585.760 ; AA his
281 CW CC NA 1 120.000 585.760 ; AA his
282 CW CC NB 1 120.000 585.760 ; AA his
283 CT CC CW 1 120.000 585.760 ; AA his
284 H5 CR NA 1 120.000 418.400 ; new99 his
285 H5 CR NB 1 120.000 418.400 ; new99 his
286 NA CR NA 1 120.000 585.760 ; AA his
287 NA CR NB 1 120.000 585.760 ; AA his
288 CC CV H4 1 120.000 418.400 ; new99 his
289 CC CV NB 1 120.000 585.760 ; AA his
290 H4 CV NB 1 120.000 418.400 ; new99 his
291 CC CW H4 1 120.000 418.400 ; new99 his
292 CC CW NA 1 120.000 585.760 ; AA his
293 H4 CW NA 1 120.000 418.400 ; new99 his
294 C* CW H4 1 120.000 418.400 ; new99 trp
295 C* CW NA 1 108.700 585.760 ; AA trp
296 CT C* CW 1 125.000 585.760 ; AA trp
297 CB C* CT 1 128.600 585.760 ; AA trp
298 CB C* CW 1 106.400 527.184 ; changed from 85.0 bsd on C6H6 nmodes; AA trp
299 CA CN NA 1 132.800 585.760 ; AA trp
300 CB CN NA 1 104.400 585.760 ; AA trp
301 CA CN CB 1 122.700 527.184 ; changed from 85.0 bsd on C6H6 nmodes; AA trp
302 C N CT 1 121.900 418.400 ; AA general
303 C N H 1 120.000 418.400 ; new99 general, gln, asn,changed based on NMA nmodes
304 CT N H 1 118.040 418.400 ; new99 general, changed based on NMA nmodes
305 CT N CT 1 118.000 418.400 ; AA pro (DETAR JACS 99,1232)
306 H N H 1 120.000 292.880 ; ade,cyt,gua,gln,asn **
307 C N* CM 1 121.600 585.760 ;
308 C N* CT 1 117.600 585.760 ;
309 C N* H 1 119.200 418.400 ; new99
310 CB N* CK 1 105.400 585.760 ;
311 CB N* CT 1 125.800 585.760 ;
312 CB N* H 1 125.800 418.400 ; new99
313 CK N* CT 1 128.800 585.760 ;
314 CK N* H 1 128.800 418.400 ; new99 for unmethylated n.a. bases,chngd bsd NMA nmodes
315 CM N* CT 1 121.200 585.760 ;
316 CM N* H 1 121.200 418.400 ; new99 for unmethylated n.a. bases,chngd bsd NMA nmodes
317 CA N2 H 1 120.000 418.400 ; new99
318 H N2 H 1 120.000 292.880 ;
319 CT N2 H 1 118.400 418.400 ; new99 arg
320 CA N2 CT 1 123.200 418.400 ; AA arg
321 CT N3 H 1 109.500 418.400 ; AA lys, changed based on NMA nmodes
322 CT N3 CT 1 109.500 418.400 ; AA pro/nt
323 H N3 H 1 109.500 292.880 ; AA lys, AA(end)
324 C NA C 1 126.400 585.760 ;
325 C NA CA 1 125.200 585.760 ;
326 C NA H 1 116.800 418.400 ; new99
327 CA NA H 1 118.000 418.400 ; new99
328 CC NA CR 1 120.000 585.760 ; AA his
329 CC NA H 1 120.000 418.400 ; new99 his
330 CR NA CW 1 120.000 585.760 ; AA his
331 CR NA H 1 120.000 418.400 ; new99 his
332 CW NA H 1 120.000 418.400 ; new99 his
333 CN NA CW 1 111.600 585.760 ; AA trp
334 CN NA H 1 123.100 418.400 ; new99 trp
335 CB NB CK 1 103.800 585.760 ;
336 CC NB CR 1 117.000 585.760 ; AA his
337 CR NB CV 1 117.000 585.760 ; AA his
338 C NC CA 1 120.500 585.760 ;
339 CA NC CB 1 112.200 585.760 ;
340 CA NC CQ 1 118.600 585.760 ;
341 CB NC CQ 1 111.000 585.760 ;
342 C OH HO 1 113.000 418.400 ; new99
343 CT OH HO 1 108.500 460.240 ;
344 HO OH P 1 108.500 376.560 ;
345 CT OS CT 1 109.500 502.080 ;
346 CT OS P 1 120.500 836.800 ;
347 P OS P 1 120.500 836.800 ;
348 O2 P OH 1 108.230 376.560 ;
349 O2 P O2 1 119.900 1171.520 ;
350 O2 P OS 1 108.230 836.800 ;
351 OH P OS 1 102.600 376.560 ;
352 OS P OS 1 102.600 376.560 ;
353 CT S CT 1 98.900 518.816 ; AA met
354 CT S S 1 103.700 569.024 ; AA cyx (SCHERAGA JPC 79,1428)
355 CT SH HS 1 96.000 359.824 ; changed from 44.0 based on methanethiol nmodes
356 HS SH HS 1 92.070 292.880 ; AA cys
357 F CT F 1 109.100 644.336 ; JCC,13,(1992),963;
358 F CT H1 1 109.500 418.400 ; new99
359 N C N 1 120.000 585.760 ; Added for Urea (same as N2-CA-N2) - EJS
361 ; New atomtype for C5' in DNA/RNA (checked with conversion and is the same as CT)
363 CT CI H1 1 109.500 418.400
364 H1 CI H1 1 109.500 292.880
365 CI CT H1 1 109.500 418.400
366 CI CT OS 1 109.500 418.400
367 CI CT CT 1 109.500 334.720
368 H1 CI OS 1 109.500 418.400
369 CT CI OS 1 109.500 418.400
370 CI OS P 1 120.500 836.800
371 H1 CI OH 1 109.500 418.400
372 CT CI OH 1 109.500 418.400
373 CI OH HO 1 108.500 460.240
376 ;i j k l func phase kd pn
377 CA CA CA OH 4 180.00 4.60240 2 ; new99
378 H5 O C OH 4 180.00 4.60240 2 ; new99
379 H5 O C OS 4 180.00 4.60240 2 ; new99
380 CM CT CM HA 4 180.00 4.60240 2 ; new99
381 CA CA CA Br 4 180.00 4.60240 2 ; new99
382 CM H4 C O 4 180.00 4.60240 2 ; new99
383 C CT N H 4 180.00 4.60240 2 ; new99
384 C CT N O 4 180.00 4.60240 2 ; new99
385 CB CK N* CT 4 180.00 4.18400 2 ;
386 CK CB N* CT 4 180.00 4.18400 2 ;
387 C CM N* CT 4 180.00 4.18400 2 ; dac guess, 9/94
388 CT N* C CM 4 180.00 4.18400 2 ;
389 CM C CM CT 4 180.00 4.60240 2 ;
390 CT O C OH 4 180.00 43.93200 2 ;
391 NA CV CC CT 4 180.00 4.60240 2 ;
392 NB CW CC CT 4 180.00 4.60240 2 ;
393 NA CW CC CT 4 180.00 4.60240 2 ;
394 CW CB C* CT 4 180.00 4.60240 2 ;
395 CA CA CA CT 4 180.00 4.60240 2 ;
396 C CM CM CT 4 180.00 4.60240 2 ; dac guess, 9/94
397 NC CM CA N2 4 180.00 4.60240 2 ; dac guess, 9/94
398 CB NC CA N2 4 180.00 4.60240 2 ; dac, 10/94
399 NA NC CA N2 4 180.00 4.60240 2 ; dac, 10/94
400 CA CA C OH 4 180.00 4.60240 2 ;
401 CT CV CC NA 4 180.00 4.60240 2 ;
402 CT CW CC NB 4 180.00 4.60240 2 ;
403 CT CW CC NA 4 180.00 4.60240 2 ;
404 CB CT C* CW 4 180.00 4.60240 2 ;
405 CM N2 CA NC 4 180.00 4.60240 2 ;
406 CB N2 CA NC 4 180.00 4.60240 2 ;
407 N2 NA CA NC 4 180.00 4.60240 2 ;
408 N N C O 4 180.00 43.93200 2 ; urea
409 X O2 C O2 4 180.00 43.93200 2 ; JCC,7,(1986),230
410 X N2 CA N2 4 180.00 43.93200 2 ; JCC,7,(1986),230
411 X CT N CT 4 180.00 4.18400 2 ; JCC,7,(1986),230
412 X X C O 4 180.00 43.93200 2 ; JCC,7,(1986),230
413 X X N H 4 180.00 4.18400 2 ; JCC,7,(1986),230
414 X X N2 H 4 180.00 4.18400 2 ; JCC,7,(1986),230
415 X X NA H 4 180.00 4.18400 2 ; JCC,7,(1986),230
416 X X CA HA 4 180.00 4.60240 2 ; bsd.on C6H6 nmodes
417 X X CW H4 4 180.00 4.60240 2 ;
418 X X CR H5 4 180.00 4.60240 2 ;
419 X X CV H4 4 180.00 4.60240 2 ;
420 X X CQ H5 4 180.00 4.60240 2 ;
421 X X CK H5 4 180.00 4.60240 2 ;
422 X X CM H4 4 180.00 4.60240 2 ;
423 X X CM HA 4 180.00 4.60240 2 ;
424 X X CA H4 4 180.00 4.60240 2 ; bsd.on C6H6 nmodes
425 X X CA H5 4 180.00 4.60240 2 ; bsd.on C6H6 nmodes
431 ; New dihedrals for C5' in DNA/RNA
433 CT OS CT CI 9 0.0 1.60247 3
434 CT OS CT CI 9 180.0 0.41840 2
435 H1 CI CT OS 9 0.0 1.04600 1
436 H1 CI CT OH 9 0.0 1.04600 1
437 H1 CT CI OS 9 0.0 1.04600 1
438 H1 CT CI OH 9 0.0 1.04600 1
439 CI CT CT CT 9 0.0 0.75312 3
440 CI CT CT CT 9 180.0 1.04600 2
441 CI CT CT CT 9 180.0 0.83680 1
443 OS P OS CI 9 31.795 0.774797 1 ; alpha (6DP after conversion, as 6DP given in paper)
444 OS P OS CI 9 351.9596 5.257326 2 ; alpha
445 OS P OS CI 9 357.24748 1.484726 3 ; alpha
446 OH P OS CI 9 31.795 0.774797 1 ; alpha
447 OH P OS CI 9 351.9596 5.257326 2 ; alpha
448 OH P OS CI 9 357.24748 1.484726 3 ; alpha
449 CT CT CI OS 9 190.97653 4.928919 1 ; gamma
450 CT CT CI OS 9 295.63279 0.385355 2 ; gamma
451 CT CT CI OS 9 348.09535 4.028481 3 ; gamma
452 CT CT CI OH 9 190.97653 4.928919 1 ; gamma
453 CT CT CI OH 9 295.63279 0.385355 2 ; gamma
454 CT CT CI OH 9 348.09535 4.028481 3 ; gamma
456 X CI OS X 9 0.0 1.60387 3
457 X CI OH X 9 0.0 0.69733 3
458 X CI CT X 9 0.0 0.65084 3
460 ; Back to normal dihedrals
462 CT CT OS CT 9 0.0 1.60247 3 ;
463 CT CT OS CT 9 180.0 0.41840 2 ;
464 C N CT C 9 0.0 1.12968 2 ; new for 99sb
465 C N CT C 9 0.0 1.75728 3 ; new for 99sb
466 N CT C N 9 180.0 1.88280 1 ; new for 99sb
467 N CT C N 9 180.0 6.61072 2 ; new for 99sb
468 N CT C N 9 180.0 2.30120 3 ; new for 99sb
469 CT CT N C 9 0.0 8.36800 1 ; new for 99sb
470 CT CT N C 9 0.0 8.36800 2 ; new for 99sb
471 CT CT N C 9 0.0 1.67360 3 ; new for 99sb
472 CT CT C N 9 0.0 0.83680 1 ; new for 99sb
473 CT CT C N 9 0.0 0.83680 2 ; new for 99sb
474 CT CT C N 9 0.0 1.67360 3 ; new for 99sb
475 H N C O 9 180.0 10.46000 2 ; JCC,7,(1986),230
476 H N C O 9 0.0 8.36800 1 ; J.C.cistrans-NMA DE
477 CT S S CT 9 0.0 14.64400 2 ; JCC,7,(1986),230
478 CT S S CT 9 0.0 2.51040 3 ; JCC,7,(1986),230
479 OS CT CT OS 9 0.0 0.60250 3 ; parm98, TC,PC,PAK
480 OS CT CT OS 9 0.0 4.91620 2 ; Piotr et al.
481 OS CT CT OH 9 0.0 0.60250 3 ; parm98, TC,PC,PAK
482 OS CT CT OH 9 0.0 4.91620 2 ; parm98, TC,PC,PAK
483 OH CT CT OH 9 0.0 0.60250 3 ; parm98, TC,PC,PAK
484 OH CT CT OH 9 0.0 4.91620 2 ; parm98, TC,PC,PAK
485 OH P OS CT 9 0.0 1.04600 3 ; JCC,7,(1986),230
486 OH P OS CT 9 0.0 5.02080 2 ; gg> ene.631g*/mp2
487 OS P OS CT 9 0.0 1.04600 3 ; JCC,7,(1986),230
488 OS P OS CT 9 0.0 5.02080 2 ; gg> ene.631g*/mp2
489 OS CT N* CK 9 0.0 10.46000 1 ; parm98, TC,PC,PAK
490 OS CT N* CM 9 0.0 10.46000 1 ; parm98, TC,PC,PAK
491 H1 CT C O 9 0.0 3.34720 1 ; Junmei et al, 1999
492 H1 CT C O 9 180.0 0.33472 3 ; Junmei et al, 1999
493 HC CT C O 9 0.0 3.34720 1 ; Junmei et al, 1999
494 HC CT C O 9 180.0 0.33472 3 ; Junmei et al, 1999
495 HC CT CT HC 9 0.0 0.62760 3 ; Junmei et al, 1999
496 HC CT CT CT 9 0.0 0.66944 3 ; Junmei et al, 1999
497 HC CT CM CM 9 180.0 1.58992 3 ; Junmei et al, 1999
498 HC CT CM CM 9 0.0 4.81160 1 ; Junmei et al, 1999
499 HO OH CT CT 9 0.0 0.66944 3 ; Junmei et al, 1999
500 HO OH CT CT 9 0.0 1.04600 1 ; Junmei et al, 1999
501 HO OH C O 9 180.0 9.62320 2 ; Junmei et al, 1999
502 HO OH C O 9 0.0 7.94960 1 ; Junmei et al, 1999
503 CM CM C O 9 180.0 9.10020 2 ; Junmei et al, 1999
504 CM CM C O 9 0.0 1.25520 3 ; Junmei et al, 1999
505 CT CM CM CT 9 180.0 27.82360 2 ; Junmei et al, 1999
506 CT CM CM CT 9 180.0 7.94960 1 ; Junmei et al, 1999
507 CT CT CT CT 9 0.0 0.75312 3 ; Junmei et al, 1999
508 CT CT CT CT 9 180.0 1.04600 2 ; Junmei et al, 1999
509 CT CT CT CT 9 180.0 0.83680 1 ; Junmei et al, 1999
510 CT CT OS C 9 0.0 1.60247 3 ; Junmei et al, 1999
511 CT CT OS C 9 180.0 3.34720 1 ; Junmei et al, 1999
512 CT OS CT OS 9 0.0 0.41840 3 ; Junmei et al, 1999
513 CT OS CT OS 9 180.0 3.55640 2 ; Junmei et al, 1999
514 CT OS CT OS 9 180.0 5.64840 1 ; Junmei et al, 1999
515 O C OS CT 9 180.0 11.29680 2 ; Junmei et al, 1999
516 O C OS CT 9 180.0 5.85760 1 ; Junmei et al, 1999
517 F CT CT F 9 180.0 5.02080 1 ; Junmei et al, 1999
518 Cl CT CT Cl 9 180.0 1.88280 1 ; Junmei et al, 1999
519 Br CT CT Br 9 0.0 0.00000 0 ; Junmei et al, 1999
520 H1 CT CT OS 9 0.0 1.04600 1 ; Junmei et al, 1999
521 H1 CT CT OH 9 0.0 1.04600 1 ; Junmei et al, 1999
522 H1 CT CT F 9 0.0 0.79496 1 ; Junmei et al, 1999
523 H1 CT CT Cl 9 0.0 1.04600 1 ; Junmei et al, 1999
524 H1 CT CT Br 9 0.0 2.30120 1 ; Junmei et al, 1999
525 HC CT CT OS 9 0.0 1.04600 1 ; Junmei et al, 1999
526 HC CT CT OH 9 0.0 1.04600 1 ; Junmei et al, 1999
527 HC CT CT F 9 0.0 0.79496 1 ; Junmei et al, 1999
528 HC CT CT Cl 9 0.0 1.04600 1 ; Junmei et al, 1999
529 HC CT CT Br 9 0.0 2.30120 1 ; Junmei et al, 1999
530 CT OS CT N* 9 0.0 1.60247 3 ; parm98.dat, TC,PC,PAK
531 CT OS CT N* 9 0.0 2.71960 2 ; Piotr et al.
532 X C C X 9 180.0 15.16700 2 ; Junmei et al, 1999
533 X C O X 9 180.0 11.71520 2 ; Junmei et al, 1999
534 X C OS X 9 180.0 11.29680 2 ; Junmei et al, 1999
535 X CA OH X 9 180.0 3.76560 2 ; Junmei et al, 99
536 X CM OS X 9 180.0 4.39320 2 ; Junmei et al, 1999
537 X C CA X 9 180.0 15.16700 2 ; intrpol.bsd.on C6H6
538 X C CB X 9 180.0 12.55200 2 ; intrpol.bsd.on C6H6
539 X C CM X 9 180.0 9.10020 2 ; intrpol.bsd.on C6H6
540 X C N* X 9 180.0 6.06680 2 ; JCC,7,(1986),230
541 X C NA X 9 180.0 5.64840 2 ; JCC,7,(1986),230
542 X C NC X 9 180.0 16.73600 2 ; JCC,7,(1986),230
543 X C OH X 9 180.0 9.62320 2 ; Junmei et al, 1999
544 X C CT X 9 0.0 0.00000 0 ; JCC,7,(1986),230
545 X CA CA X 9 180.0 15.16700 2 ; intrpol.bsd.on C6H6
546 X CA CB X 9 180.0 14.64400 2 ; intrpol.bsd.on C6H6
547 X CA CM X 9 180.0 10.66920 2 ; intrpol.bsd.on C6H6
548 X CA CT X 9 0.0 0.00000 0 ; JCC,7,(1986),230
549 X CA N2 X 9 180.0 10.04160 2 ; reinterpolated 93'
550 X CA NA X 9 180.0 6.27600 2 ; JCC,7,(1986),230
551 X CA NC X 9 180.0 20.08320 2 ; JCC,7,(1986),230
552 X CB CB X 9 180.0 22.80280 2 ; intrpol.bsd.on C6H6
553 X CB N* X 9 180.0 6.90360 2 ; JCC,7,(1986),230
554 X CB NB X 9 180.0 10.66920 2 ; JCC,7,(1986),230
555 X CB NC X 9 180.0 17.36360 2 ; JCC,7,(1986),230
556 X CK N* X 9 180.0 7.11280 2 ; JCC,7,(1986),230
557 X CK NB X 9 180.0 41.84000 2 ; JCC,7,(1986),230
558 X CM CM X 9 180.0 27.82360 2 ; intrpol.bsd.on C6H6
559 X CM CT X 9 0.0 0.00000 0 ; JCC,7,(1986),230
560 X CM N* X 9 180.0 7.74040 2 ; JCC,7,(1986),230
561 X CQ NC X 9 180.0 28.45120 2 ; JCC,7,(1986),230
562 X CT CT X 9 0.0 0.65084 3 ; JCC,7,(1986),230
563 X CT N X 9 0.0 0.00000 0 ; JCC,7,(1986),230
564 X CT N* X 9 0.0 0.00000 0 ; JCC,7,(1986),230
565 X CT N2 X 9 0.0 0.00000 0 ; JCC,7,(1986),230
566 X CT OH X 9 0.0 0.69733 3 ; JCC,7,(1986),230
567 X CT OS X 9 0.0 1.60387 3 ; JCC,7,(1986),230
568 X OH P X 9 0.0 1.04600 3 ; JCC,7,(1986),230
569 X OS P X 9 0.0 1.04600 3 ; JCC,7,(1986),230
570 X C N X 9 180.0 10.46000 2 ; AA,NMA
571 X CT N3 X 9 0.0 0.65084 3 ; JCC,7,(1986),230
572 X CT S X 9 0.0 1.39467 3 ; JCC,7,(1986),230
573 X CT SH X 9 0.0 1.04600 3 ; JCC,7,(1986),230
574 X C* CB X 9 180.0 7.00820 2 ; intrpol.bsd.onC6H6aa
575 X C* CT X 9 0.0 0.00000 0 ; JCC,7,(1986),230
576 X C* CW X 9 180.0 27.30060 2 ; intrpol.bsd.on C6H6
577 X CA CN X 9 180.0 15.16700 2 ; reinterpolated 93'
578 X CB CN X 9 180.0 12.55200 2 ; reinterpolated 93'
579 X CC CT X 9 0.0 0.00000 0 ; JCC,7,(1986),230
580 X CC CV X 9 180.0 21.54760 2 ; intrpol.bsd.on C6H6
581 X CC CW X 9 180.0 22.48900 2 ; intrpol.bsd.on C6H6
582 X CC NA X 9 180.0 5.85760 2 ; JCC,7,(1986),230
583 X CC NB X 9 180.0 10.04160 2 ; JCC,7,(1986),230
584 X CN NA X 9 180.0 6.38060 2 ; reinterpolated 93'
585 X CR NA X 9 180.0 9.72780 2 ; JCC,7,(1986),230
586 X CR NB X 9 180.0 20.92000 2 ; JCC,7,(1986),230
587 X CV NB X 9 180.0 10.04160 2 ; JCC,7,(1986),230
588 X CW NA X 9 180.0 6.27600 2 ; JCC,7,(1986),230
589 ; Modified amino acid torsions in Amber99SB-ILDN
590 ; These should not override the general torsion for the atom types,
591 ; so to avoid introducing extra new atom types we list them explicitly for
592 ; the residues in question:
594 #define torsion_ILE_N_CA_CB_CG2_mult1 0.0 0.8158800 1 ; Proteins 78, 1950 (2010)
595 #define torsion_ILE_N_CA_CB_CG2_mult2 0.0 -3.5396640 2 ; Proteins 78, 1950 (2010)
597 #define torsion_LEU_C_CA_CB_CG_mult1 0.0 2.3890640 1 ; Proteins 78, 1950 (2010)
598 #define torsion_LEU_C_CA_CB_CG_mult2 0.0 -1.4978720 2 ; Proteins 78, 1950 (2010)
599 #define torsion_LEU_C_CA_CB_CG_mult3 0.0 0.5648400 3 ; Proteins 78, 1950 (2010)
601 #define torsion_ASP_N_CA_CB_CG_mult1 0.0 -11.024840 1 ; Proteins 78, 1950 (2010)
602 #define torsion_ASP_N_CA_CB_CG_mult2 0.0 -4.978960 2 ; Proteins 78, 1950 (2010)
603 #define torsion_ASP_N_CA_CB_CG_mult3 0.0 -0.029288 3 ; Proteins 78, 1950 (2010)
604 #define torsion_ASP_N_CA_CB_CG_mult4 0.0 1.769832 4 ; Proteins 78, 1950 (2010)
605 #define torsion_ASP_N_CA_CB_CG_mult5 0.0 0.970688 5 ; Proteins 78, 1950 (2010)
606 #define torsion_ASP_N_CA_CB_CG_mult6 0.0 -0.891192 6 ; Proteins 78, 1950 (2010)
608 #define torsion_ASP_CA_CB_CG_OD_mult1 0.0 0.0 1 ; Proteins 78, 1950 (2010)
609 #define torsion_ASP_CA_CB_CG_OD_mult2 0.0 -1.853512 2 ; Proteins 78, 1950 (2010)
610 #define torsion_ASP_CA_CB_CG_OD_mult3 0.0 0.0 3 ; Proteins 78, 1950 (2010)
611 #define torsion_ASP_CA_CB_CG_OD_mult4 0.0 -0.577392 4 ; Proteins 78, 1950 (2010)
612 #define torsion_ASP_CA_CB_CG_OD_mult5 0.0 0.0 5 ; Proteins 78, 1950 (2010)
613 #define torsion_ASP_CA_CB_CG_OD_mult6 0.0 -0.054392 6 ; Proteins 78, 1950 (2010)
615 #define torsion_ASN_C_CA_CB_CG_mult1 0.0 2.389064 1 ; Proteins 78, 1950 (2010)
616 #define torsion_ASN_C_CA_CB_CG_mult2 0.0 -2.493664 2 ; Proteins 78, 1950 (2010)
617 #define torsion_ASN_C_CA_CB_CG_mult3 0.0 0.493712 3 ; Proteins 78, 1950 (2010)
618 #define torsion_ASN_C_CA_CB_CG_mult4 0.0 -1.744728 4 ; Proteins 78, 1950 (2010)
619 #define torsion_ASN_C_CA_CB_CG_mult5 0.0 0.435136 5 ; Proteins 78, 1950 (2010)
620 #define torsion_ASN_C_CA_CB_CG_mult6 0.0 -0.422584 6 ; Proteins 78, 1950 (2010)
622 #define torsion_ASN_CA_CB_CG_ND2_mult1 0.0 -4.376464 1 ; Proteins 78, 1950 (2010)
623 #define torsion_ASN_CA_CB_CG_ND2_mult2 0.0 -0.757304 2 ; Proteins 78, 1950 (2010)
624 #define torsion_ASN_CA_CB_CG_ND2_mult3 0.0 -0.146440 3 ; Proteins 78, 1950 (2010)
625 #define torsion_ASN_CA_CB_CG_ND2_mult4 0.0 0.418400 4 ; Proteins 78, 1950 (2010)
626 #define torsion_ASN_CA_CB_CG_ND2_mult5 0.0 0.543920 5 ; Proteins 78, 1950 (2010)
627 #define torsion_ASN_CA_CB_CG_ND2_mult6 0.0 -0.443504 6 ; Proteins 78, 1950 (2010)
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