1PARM96 for DNA, RNA and proteins with TIP3P Water. USE SCEE=1.2 in energy progs 2BR 79.90 ! bromine 3C 12.01 sp2 C carbonyl group 4CA 12.01 sp2 C pure aromatic (benzene) 5CB 12.01 sp2 aromatic C, 5&6 membered ring junction 6CC 12.01 sp2 aromatic C, 5 memb. ring HIS 7CK 12.01 sp2 C 5 memb.ring in purines 8CM 12.01 sp2 C pyrimidines in pos. 5 & 6 9CN 12.01 sp2 C aromatic 5&6 memb.ring junct.(TRP) 10CQ 12.01 sp2 C in 5 mem.ring of purines between 2 N 11CR 12.01 sp2 arom as CQ but in HIS 12CT 12.01 sp3 aliphatic C 13CV 12.01 sp2 arom. 5 memb.ring w/1 N and 1 H (HIS) 14CW 12.01 sp2 arom. 5 memb.ring w/1 N-H and 1 H (HIS) 15C* 12.01 sp2 arom. 5 memb.ring w/1 subst. (TRP) 16C0 40.08 calcium 17F 19.00 fluorine 18H 1.008 H bonded to nitrogen atoms 19HC 1.008 H aliph. bond. to C without electrwd.group 20H1 1.008 H aliph. bond. to C with 1 electrwd. group 21H2 1.008 H aliph. bond. to C with 2 electrwd.groups 22H3 1.008 H aliph. bond. to C with 3 eletrwd.groups 23HA 1.008 H arom. bond. to C without elctrwd. groups 24H4 1.008 H arom. bond. to C with 1 electrwd. group 25H5 1.008 H arom. bond. to C with 2 electrwd. groups 26HO 1.008 hydroxyl group 27HS 1.008 hydrogen bonded to sulphur 28HW 1.008 H in TIP3P water 29HP 1.008 H bonded to C next to positively charged gr 30I 126.9 iodine 31IM 35.45 assumed to be Cl- 32IP 22.99 assumed to be Na+ 33IB 131.0 'big ion w/ waters' for vacuum (Na+, 6H2O) 34MG 24.305 magnesium 35N 14.01 sp2 nitrogen in amide groups 36NA 14.01 sp2 N in 5 memb.ring w/H atom (HIS) 37NB 14.01 sp2 N in 5 memb.ring w/LP (HIS,ADE,GUA) 38NC 14.01 sp2 N in 6 memb.ring w/LP (ADE,GUA) 39N2 14.01 sp2 N in amino groups 40N3 14.01 sp3 N for charged amino groups (Lys, etc) 41N* 14.01 sp2 N 42O 16.00 carbonyl group oxygen 43OW 16.00 oxygen in TIP3P water 44OH 16.00 oxygen in hydroxyl group 45OS 16.00 ether and ester oxygen 46O2 16.00 carboxyl and phosphate group oxygen 47P 30.97 phosphate 48S 32.06 sulphur in disulfide linkage 49SH 32.06 sulphur in cystine 50CU 63.55 copper 51FE 55.00 iron 52Li 6.94 lithium 53K 39.10 potassium 54Rb 85.47 rubidium 55Cs 132.91 cesium 56 57C H HO N NA NB NC N2 NT N2 N3 N* O OH OS P O2 58OW-HW 553.0 0.9572 ! TIP3P water 59HW-HW 553.0 1.5136 TIP3P water 60C -CA 469.0 1.409 JCC,7,(1986),230; TYR 61C -CB 447.0 1.419 JCC,7,(1986),230; GUA 62C -CM 410.0 1.444 JCC,7,(1986),230; THY,URA 63C -CT 317.0 1.522 JCC,7,(1986),230; AA 64C -N* 424.0 1.383 JCC,7,(1986),230; CYT,URA 65C -NA 418.0 1.388 JCC,7,(1986),230; GUA.URA 66C -NC 457.0 1.358 JCC,7,(1986),230; CYT 67C -O 570.0 1.229 JCC,7,(1986),230; AA,CYT,GUA,THY,URA 68C -O2 656.0 1.250 JCC,7,(1986),230; GLU,ASP 69C -OH 450.0 1.364 JCC,7,(1986),230; TYR 70CA-CA 469.0 1.400 JCC,7,(1986),230; BENZENE,PHE,TRP,TYR 71CA-CB 469.0 1.404 JCC,7,(1986),230; ADE,TRP 72CA-CM 427.0 1.433 JCC,7,(1986),230; CYT 73CA-CT 317.0 1.510 JCC,7,(1986),230; PHE,TYR 74CA-HA 367.0 1.080 changed from 340. bsd on C6H6 nmodes; PHE,TRP,TYR 75CA-H4 367.0 1.080 changed from 340. bsd on C6H6 nmodes; no assigned 76CA-N2 481.0 1.340 JCC,7,(1986),230; ARG,CYT,GUA 77CA-NA 427.0 1.381 JCC,7,(1986),230; GUA 78CA-NC 483.0 1.339 JCC,7,(1986),230; ADE,CYT,GUA 79CB-CB 520.0 1.370 JCC,7,(1986),230; ADE,GUA 80CB-N* 436.0 1.374 JCC,7,(1986),230; ADE,GUA 81CB-NB 414.0 1.391 JCC,7,(1986),230; ADE,GUA 82CB-NC 461.0 1.354 JCC,7,(1986),230; ADE,GUA 83CK-H5 367.0 1.080 changed from 340. bsd on C6H6 nmodes; ADE,GUA 84CK-N* 440.0 1.371 JCC,7,(1986),230; ADE,GUA 85CK-NB 529.0 1.304 JCC,7,(1986),230; ADE,GUA 86CM-CM 549.0 1.350 JCC,7,(1986),230; CYT,THY,URA 87CM-CT 317.0 1.510 JCC,7,(1986),230; THY 88CM-HA 367.0 1.080 changed from 340. bsd on C6H6 nmodes; CYT,URA 89CM-H4 367.0 1.080 changed from 340. bsd on C6H6 nmodes; CYT,URA 90CM-H5 367.0 1.080 changed from 340. bsd on C6H6 nmodes; not assigned 91CM-N* 448.0 1.365 JCC,7,(1986),230; CYT,THY,URA 92CQ-H5 367.0 1.080 changed from 340. bsd on C6H6 nmodes; ADE 93CQ-NC 502.0 1.324 JCC,7,(1986),230; ADE 94CT-CT 310.0 1.526 JCC,7,(1986),230; AA, SUGARS 95CT-HC 340.0 1.090 changed from 331 bsd on NMA nmodes; AA, SUGARS 96CT-H1 340.0 1.090 changed from 331 bsd on NMA nmodes; AA, RIBOSE 97CT-H2 340.0 1.090 changed from 331 bsd on NMA nmodes; SUGARS 98CT-H3 340.0 1.090 changed from 331 bsd on NMA nmodes; not assigned 99CT-HP 340.0 1.090 changed from 331; AA-lysine, methyl ammonium cation 100CT-N* 337.0 1.475 JCC,7,(1986),230; ADE,CYT,GUA,THY,URA 101CT-N2 337.0 1.463 JCC,7,(1986),230; ARG 102CT-OH 320.0 1.410 JCC,7,(1986),230; SUGARS 103CT-OS 320.0 1.410 JCC,7,(1986),230; NUCLEIC ACIDS 104H -N2 434.0 1.010 JCC,7,(1986),230; ADE,CYT,GUA,ARG 105H -N* 434.0 1.010 for plain unmethylated bases ADE,CYT,GUA,ARG 106H -NA 434.0 1.010 JCC,7,(1986),230; GUA,URA,HIS 107HO-OH 553.0 0.960 JCC,7,(1986),230; SUGARS,SER,TYR 108HO-OS 553.0 0.960 JCC,7,(1986),230; NUCLEOTIDE ENDS 109O2-P 525.0 1.480 JCC,7,(1986),230; NA PHOSPHATES 110OH-P 230.0 1.610 JCC,7,(1986),230; NA PHOSPHATES 111OS-P 230.0 1.610 JCC,7,(1986),230; NA PHOSPHATES 112C*-HC 367.0 1.080 changed from 340. bsd on C6H6 nmodes, not needed AA 113C -N 490.0 1.335 JCC,7,(1986),230; AA 114C*-CB 388.0 1.459 JCC,7,(1986),230; TRP 115C*-CT 317.0 1.495 JCC,7,(1986),230; TRP 116C*-CW 546.0 1.352 JCC,7,(1986),230; TRP 117CA-CN 469.0 1.400 JCC,7,(1986),230; TRP 118CB-CN 447.0 1.419 JCC,7,(1986),230; TRP 119CC-CT 317.0 1.504 JCC,7,(1986),230; HIS 120CC-CV 512.0 1.375 JCC,7,(1986),230; HIS(delta) 121CC-CW 518.0 1.371 JCC,7,(1986),230; HIS(epsilon) 122CC-NA 422.0 1.385 JCC,7,(1986),230; HIS 123CC-NB 410.0 1.394 JCC,7,(1986),230; HIS 124CN-NA 428.0 1.380 JCC,7,(1986),230; TRP 125CR-H5 367.0 1.080 changed from 340. bsd on C6H6 nmodes;HIS 126CR-NA 477.0 1.343 JCC,7,(1986),230; HIS 127CR-NB 488.0 1.335 JCC,7,(1986),230; HIS 128CT-N 337.0 1.449 JCC,7,(1986),230; AA 129CT-N3 367.0 1.471 JCC,7,(1986),230; LYS 130CT-S 227.0 1.810 changed from 222.0 based on dimethylS nmodes 131CT-SH 237.0 1.810 changed from 222.0 based on methanethiol nmodes 132CV-H4 367.0 1.080 changed from 340. bsd on C6H6 nmodes; HIS 133CV-NB 410.0 1.394 JCC,7,(1986),230; HIS 134CW-H4 367.0 1.080 changed from 340. bsd on C6H6 nmodes;HIS(epsilon,+) 135CW-NA 427.0 1.381 JCC,7,(1986),230; HIS,TRP 136H -N 434.0 1.010 JCC,7,(1986),230; AA 137H -N3 434.0 1.010 JCC,7,(1986),230; LYS 138HS-SH 274.0 1.336 JCC,7,(1986),230; CYS 139S -S 166.0 2.038 JCC,7,(1986),230; CYX (SCHERAGA) 140CT-F 367.0 1.380 JCC,13,(1992),963;CF4; R0=1.332 FOR CHF3 141 142HW-OW-HW 100. 104.52 TIP3P water 143HW-HW-OW 0. 127.74 (found in crystallographic water with 3 bonds) 144CB-C -NA 70.0 111.30 NA 145CB-C -O 80.0 128.80 146CM-C -NA 70.0 114.10 147CM-C -O 80.0 125.30 148CT-C -O 80.0 120.40 149CT-C -O2 70.0 117.00 150CT-C -OH 70.0 117.00 151N*-C -NA 70.0 115.40 152N*-C -NC 70.0 118.60 153N*-C -O 80.0 120.90 154NA-C -O 80.0 120.60 155NC-C -O 80.0 122.50 156CT-C -N 70.0 116.60 AA general 157N -C -O 80.0 122.90 AA general 158O -C -O 80.0 126.00 AA COO- terminal residues 159O2-C -O2 80.0 126.00 AA GLU (SCH JPC 79,2379) 160O -C -OH 80.0 126.00 161CA-C -CA 63.0 120.00 changed from 85.0 bsd on C6H6 nmodes; AA tyr 162CA-C -OH 70.0 120.00 AA tyr 163C -CA-CA 63.0 120.00 changed from 85.0 bsd on C6H6 nmodes 164CA-CA-CA 63.0 120.00 changed from 85.0 bsd on C6H6 nmodes 165CA-CA-CB 63.0 120.00 changed from 85.0 bsd on C6H6 nmodes 166CA-CA-CT 70.0 120.00 167CA-CA-HA 35.0 120.00 168CA-CA-H4 35.0 120.00 169CB-CA-HA 35.0 120.00 170CB-CA-H4 35.0 120.00 171CB-CA-N2 70.0 123.50 172CB-CA-NC 70.0 117.30 173CM-CA-N2 70.0 120.10 174CM-CA-NC 70.0 121.50 175N2-CA-NA 70.0 116.00 176N2-CA-NC 70.0 119.30 177NA-CA-NC 70.0 123.30 178C -CA-HA 35.0 120.00 AA tyr 179N2-CA-N2 70.0 120.00 AA arg 180CN-CA-HA 35.0 120.00 AA trp 181CA-CA-CN 63.0 120.00 changed from 85.0 bsd on C6H6 nmodes; AA trp 182C -CB-CB 63.0 119.20 changed from 85.0 bsd on C6H6 nmodes; NA gua 183C -CB-NB 70.0 130.00 184CA-CB-CB 63.0 117.30 changed from 85.0 bsd on C6H6 nmodes; NA ade 185CA-CB-NB 70.0 132.40 186CB-CB-N* 70.0 106.20 187CB-CB-NB 70.0 110.40 188CB-CB-NC 70.0 127.70 189N*-CB-NC 70.0 126.20 190C*-CB-CA 63.0 134.90 changed from 85.0 bsd on C6H6 nmodes; AA trp 191C*-CB-CN 63.0 108.80 changed from 85.0 bsd on C6H6 nmodes; AA trp 192CA-CB-CN 63.0 116.20 changed from 85.0 bsd on C6H6 nmodes; AA trp 193H5-CK-N* 35.0 123.05 194H5-CK-NB 35.0 123.05 195N*-CK-NB 70.0 113.90 196C -CM-CM 63.0 120.70 changed from 85.0 bsd on C6H6 nmodes; NA thy 197C -CM-CT 70.0 119.70 198C -CM-HA 35.0 119.70 199C -CM-H4 35.0 119.70 200CA-CM-CM 63.0 117.00 changed from 85.0 bsd on C6H6 nmodes; NA cyt 201CA-CM-HA 35.0 123.30 202CA-CM-H4 35.0 123.30 203CM-CM-CT 70.0 119.70 204CM-CM-HA 35.0 119.70 205CM-CM-H4 35.0 119.70 206CM-CM-N* 70.0 121.20 207H4-CM-N* 35.0 119.10 208H5-CQ-NC 35.0 115.45 209NC-CQ-NC 70.0 129.10 210CM-CT-HC 50.0 109.50 changed based on NMA nmodes 211CT-CT-CT 40.0 109.50 212CT-CT-HC 50.0 109.50 changed based on NMA nmodes 213CT-CT-H1 50.0 109.50 changed based on NMA nmodes 214CT-CT-H2 50.0 109.50 changed based on NMA nmodes 215CT-CT-HP 50.0 109.50 changed based on NMA nmodes 216CT-CT-N* 50.0 109.50 217CT-CT-OH 50.0 109.50 218CT-CT-OS 50.0 109.50 219HC-CT-HC 35.0 109.50 220H1-CT-H1 35.0 109.50 221HP-CT-HP 35.0 109.50 AA lys, ch3nh4+ 222H2-CT-N* 50.0 109.50 changed based on NMA nmodes 223H1-CT-N* 50.0 109.50 changed based on NMA nmodes 224H1-CT-OH 50.0 109.50 changed based on NMA nmodes 225H1-CT-OS 50.0 109.50 changed based on NMA nmodes 226H2-CT-OS 50.0 109.50 changed based on NMA nmodes 227N*-CT-OS 50.0 109.50 228H1-CT-N 50.0 109.50 AA general changed based on NMA nmodes 229C -CT-H1 50.0 109.50 AA general changed based on NMA nmodes 230C -CT-HP 50.0 109.50 AA zwitterion changed based on NMA nmodes 231H1-CT-S 50.0 109.50 AA cys changed based on NMA nmodes 232H1-CT-SH 50.0 109.50 AA cyx changed based on NMA nmodes 233CT-CT-S 50.0 114.70 AA cyx (SCHERAGA JPC 79,1428) 234CT-CT-SH 50.0 108.60 AA cys 235H2-CT-H2 35.0 109.50 AA lys 236H1-CT-N2 50.0 109.50 AA arg changed based on NMA nmodes 237HP-CT-N3 50.0 109.50 AA lys, ch3nh3+, changed based on NMA nmodes 238CA-CT-CT 63.0 114.00 AA phe tyr (SCH JPC 79,2379) 239C -CT-HC 50.0 109.50 AA gln changed based on NMA nmodes 240C -CT-N 63.0 110.10 AA general 241CT-CT-N2 80.0 111.20 AA arg (JCP 76, 1439) 242CT-CT-N 80.0 109.70 AA ala, general (JACS 94, 2657) 243C -CT-CT 63.0 111.10 AA general 244CA-CT-HC 50.0 109.50 AA tyr changed based on NMA nmodes 245CT-CT-N3 80.0 111.20 AA lys (JCP 76, 1439) 246CC-CT-CT 63.0 113.10 AA his 247CC-CT-HC 50.0 109.50 AA his changed based on NMA nmodes 248C -CT-N3 80.0 111.20 AA amino terminal residues 249C*-CT-CT 63.0 115.60 AA trp 250C*-CT-HC 50.0 109.50 AA trp changed based on NMA nmodes 251CT-CC-NA 70.0 120.00 AA his 252CT-CC-CV 70.0 120.00 AA his 253CT-CC-NB 70.0 120.00 AA his 254CV-CC-NA 70.0 120.00 AA his 255CW-CC-NA 70.0 120.00 AA his 256CW-CC-NB 70.0 120.00 AA his 257CT-CC-CW 70.0 120.00 AA his 258H5-CR-NA 35.0 120.00 AA his 259H5-CR-NB 35.0 120.00 AA his 260NA-CR-NA 70.0 120.00 AA his 261NA-CR-NB 70.0 120.00 AA his 262CC-CV-H4 35.0 120.00 AA his 263CC-CV-NB 70.0 120.00 AA his 264H4-CV-NB 35.0 120.00 AA his 265CC-CW-H4 35.0 120.00 AA his 266CC-CW-NA 70.0 120.00 AA his 267H4-CW-NA 35.0 120.00 AA his 268C*-CW-H4 35.0 120.00 AA trp 269C*-CW-NA 70.0 108.70 AA trp 270CT-C*-CW 70.0 125.00 AA trp 271CB-C*-CT 70.0 128.60 AA trp 272CB-C*-CW 63.0 106.40 changed from 85.0 bsd on C6H6 nmodes; AA trp 273CA-CN-NA 70.0 132.80 AA trp 274CB-CN-NA 70.0 104.40 AA trp 275CA-CN-CB 63.0 122.70 changed from 85.0 bsd on C6H6 nmodes; AA trp 276C -N -CT 50.0 121.90 AA general 277C -N -H 30.0 120.00 AA general, gln, asn,changed based on NMA nmodes 278CT-N -H 30.0 118.04 AA general, changed based on NMA nmodes 279CT-N -CT 50.0 118.00 AA pro (DETAR JACS 99,1232) 280H -N -H 35.0 120.00 ade,cyt,gua,gln,asn ** 281C -N*-CM 70.0 121.60 282C -N*-CT 70.0 117.60 283C -N*-H 30.0 119.20 changed based on NMA nmodes 284CB-N*-CK 70.0 105.40 285CB-N*-CT 70.0 125.80 286CB-N*-H 30.0 125.80 for unmethylated n.a. bases,chngd bsd NMA nmodes 287CK-N*-CT 70.0 128.80 288CK-N*-H 30.0 128.80 for unmethylated n.a. bases,chngd bsd NMA nmodes 289CM-N*-CT 70.0 121.20 290CM-N*-H 30.0 121.20 for unmethylated n.a. bases,chngd bsd NMA nmodes 291CA-N2-H 35.0 120.00 292H -N2-H 35.0 120.00 293CT-N2-H 35.0 118.40 AA arg 294CA-N2-CT 50.0 123.20 AA arg 295CT-N3-H 50.0 109.50 AA lys, changed based on NMA nmodes 296CT-N3-CT 50.0 109.50 AA pro/nt 297H -N3-H 35.0 109.50 AA lys, AA(end) 298C -NA-C 70.0 126.40 299C -NA-CA 70.0 125.20 300C -NA-H 30.0 116.80 changed based on NMA nmodes 301CA-NA-H 30.0 118.00 changed based on NMA nmodes 302CC-NA-CR 70.0 120.00 AA his 303CC-NA-H 30.0 120.00 AA his, changed based on NMA nmodes 304CR-NA-CW 70.0 120.00 AA his 305CR-NA-H 30.0 120.00 AA his, changed based on NMA nmodes 306CW-NA-H 30.0 120.00 AA his, changed based on NMA nmodes 307CN-NA-CW 70.0 111.60 AA trp 308CN-NA-H 30.0 123.10 AA trp, changed based on NMA nmodes 309CB-NB-CK 70.0 103.80 310CC-NB-CR 70.0 117.00 AA his 311CR-NB-CV 70.0 117.00 AA his 312C -NC-CA 70.0 120.50 313CA-NC-CB 70.0 112.20 314CA-NC-CQ 70.0 118.60 315CB-NC-CQ 70.0 111.00 316C -OH-HO 35.0 113.00 317CT-OH-HO 55.0 108.50 318HO-OH-P 45.0 108.50 319CT-OS-CT 60.0 109.50 320CT-OS-P 100.0 120.50 321P -OS-P 100.0 120.50 322O2-P -OH 45.0 108.23 323O2-P -O2 140.0 119.90 324O2-P -OS 100.0 108.23 325OH-P -OS 45.0 102.60 326OS-P -OS 45.0 102.60 327CT-S -CT 62.0 98.90 AA met 328CT-S -S 68.0 103.70 AA cyx (SCHERAGA JPC 79,1428) 329CT-SH-HS 43.0 96.00 changed from 44.0 based on methanethiol nmodes 330HS-SH-HS 35.0 92.07 AA cys 331F -CT-F 77.0 109.10 JCC,13,(1992),963; 332F -CT-H1 35.0 109.50 JCC,13,(1992),963; 333 334X -C -CA-X 4 14.50 180.0 2. intrpol.bsd.on C6H6 335X -C -CB-X 4 12.00 180.0 2. intrpol.bsd.on C6H6 336X -C -CM-X 4 8.70 180.0 2. intrpol.bsd.on C6H6 337X -C -N*-X 4 5.80 180.0 2. JCC,7,(1986),230 338X -C -NA-X 4 5.40 180.0 2. JCC,7,(1986),230 339X -C -NC-X 2 8.00 180.0 2. JCC,7,(1986),230 340X -C -OH-X 2 1.80 180.0 2. JCC,7,(1986),230 341X -C -CT-X 4 0.00 0.0 2. JCC,7,(1986),230 342X -CA-CA-X 4 14.50 180.0 2. intrpol.bsd.on C6H6 343X -CA-CB-X 4 14.00 180.0 2. intrpol.bsd.on C6H6 344X -CA-CM-X 4 10.20 180.0 2. intrpol.bsd.on C6H6 345X -CA-CT-X 6 0.00 0.0 2. JCC,7,(1986),230 346X -CA-N2-X 4 9.60 180.0 2. reinterpolated 93' 347X -CA-NA-X 4 6.00 180.0 2. JCC,7,(1986),230 348X -CA-NC-X 2 9.60 180.0 2. JCC,7,(1986),230 349X -CB-CB-X 4 21.80 180.0 2. intrpol.bsd.on C6H6 350X -CB-N*-X 4 6.60 180.0 2. JCC,7,(1986),230 351X -CB-NB-X 2 5.10 180.0 2. JCC,7,(1986),230 352X -CB-NC-X 2 8.30 180.0 2. JCC,7,(1986),230 353X -CK-N*-X 4 6.80 180.0 2. JCC,7,(1986),230 354X -CK-NB-X 2 20.00 180.0 2. JCC,7,(1986),230 355X -CM-CM-X 4 26.60 180.0 2. intrpol.bsd.on C6H6 356X -CM-CT-X 6 0.00 0.0 3. JCC,7,(1986),230 357X -CM-N*-X 4 7.40 180.0 2. JCC,7,(1986),230 358X -CQ-NC-X 2 13.60 180.0 2. JCC,7,(1986),230 359X -CT-CT-X 9 1.40 0.0 3. JCC,7,(1986),230 360X -CT-N -X 6 0.00 0.0 2. JCC,7,(1986),230 361X -CT-N*-X 6 0.00 0.0 2. JCC,7,(1986),230 362X -CT-N2-X 6 0.00 0.0 3. JCC,7,(1986),230 363X -CT-OH-X 3 0.50 0.0 3. JCC,7,(1986),230 364X -CT-OS-X 3 1.15 0.0 3. JCC,7,(1986),230 365X -OH-P -X 3 0.75 0.0 3. JCC,7,(1986),230 366X -OS-P -X 3 0.75 0.0 3. JCC,7,(1986),230 367X -C -N -X 4 10.00 180.0 2. AA|check Wendy?&NMA 368X -CT-N3-X 9 1.40 0.0 3. JCC,7,(1986),230 369X -CT-S -X 3 1.00 0.0 3. JCC,7,(1986),230 370X -CT-SH-X 3 0.75 0.0 3. JCC,7,(1986),230 371X -C*-CB-X 4 6.70 180.0 2. intrpol.bsd.onC6H6aa 372X -C*-CT-X 6 0.00 0.0 2. JCC,7,(1986),230 373X -C*-CW-X 4 26.10 180.0 2. intrpol.bsd.on C6H6 374X -CA-CN-X 4 14.50 180.0 2. reinterpolated 93' 375X -CB-CN-X 4 12.00 180.0 2. reinterpolated 93' 376X -CC-CT-X 6 0.00 0.0 2. JCC,7,(1986),230 377X -CC-CV-X 4 20.60 180.0 2. intrpol.bsd.on C6H6 378X -CC-CW-X 4 21.50 180.0 2. intrpol.bsd.on C6H6 379X -CC-NA-X 4 5.60 180.0 2. JCC,7,(1986),230 380X -CC-NB-X 2 4.80 180.0 2. JCC,7,(1986),230 381X -CN-NA-X 4 6.10 180.0 2. reinterpolated 93' 382X -CR-NA-X 4 9.30 180.0 2. JCC,7,(1986),230 383X -CR-NB-X 2 10.00 180.0 2. JCC,7,(1986),230 384X -CV-NB-X 2 4.80 180.0 2. JCC,7,(1986),230 385X -CW-NA-X 4 6.00 180.0 2. JCC,7,(1986),230 386CT-CT-OS-CT 1 0.383 0.0 -3. 387CT-CT-OS-CT 1 0.1 180.0 2. 388C -N -CT-C 1 0.30 180.0 -2. Kollman et al. 1997 389C -N -CT-C 1 0.85 000.0 1. Kollman et al. 1997 390N -CT-C -N 1 0.30 180.0 -2. Kollman et al. 1997 391N -CT-C -N 1 0.85 000.0 1. Kollman et al. 1997 392CT-CT-N -C 1 0.50 180.0 -4. 393CT-CT-N -C 1 0.15 180.0 -3. 394CT-CT-N -C 1 0.53 0.0 1. 395CT-CT-C -N 1 0.100 0.0 -4. 396CT-CT-C -N 1 0.07 0.0 2. 397H -N -C -O 1 2.50 180.0 -2. JCC,7,(1986),230 398H -N -C -O 1 2.00 0.0 1. J.C.cistrans-NMA DE 399CT-S -S -CT 1 3.50 0.0 -2. JCC,7,(1986),230 400CT-S -S -CT 1 0.60 0.0 3. JCC,7,(1986),230 401OS-CT-CT-OS 1 0.144 0.0 -3. JCC,7,(1986),230 402OS-CT-CT-OS 1 1.00 0.0 2. pucker anal (93') 403OS-CT-CT-OH 1 0.144 0.0 -3. JCC,7,(1986),230 404OS-CT-CT-OH 1 1.00 0.0 2. pucker anal (93') 405OH-CT-CT-OH 1 0.144 0.0 -3. JCC,7,(1986),230 406OH-CT-CT-OH 1 1.00 0.0 2. check glicolWC? puc 407OH-P -OS-CT 1 0.25 0.0 -3. JCC,7,(1986),230 408OH-P -OS-CT 1 1.20 0.0 2. gg> ene.631g*/mp2 409OS-P -OS-CT 1 0.25 0.0 -3. JCC,7,(1986),230 410OS-P -OS-CT 1 1.20 0.0 2. gg> ene.631g*/mp2 411OS-CT-N*-CK 1 0.50 180.0 -2. sugar frag calc (PC) 412OS-CT-N*-CK 1 2.50 0.0 1. sugar frag calc (PC) 413OS-CT-N*-CM 1 0.50 180.0 -2. sugar frag calc (PC) 414OS-CT-N*-CM 1 2.50 0.0 1. sugar frag calc (PC) 415 416X -X -C -O 10.5 180. 2. JCC,7,(1986),230 417X -O2-C -O2 10.5 180. 2. JCC,7,(1986),230 418X -X -N -H 1.0 180. 2. JCC,7,(1986),230 419X -X -N2-H 1.0 180. 2. JCC,7,(1986),230 420X -X -NA-H 1.0 180. 2. JCC,7,(1986),230 421X -N2-CA-N2 10.5 180. 2. JCC,7,(1986),230 422X -CT-N -CT 1.0 180. 2. JCC,7,(1986),230 423X -X -CA-HA 1.1 180. 2. bsd.on C6H6 nmodes 424X -X -CW-H4 1.1 180. 2. 425X -X -CR-H5 1.1 180. 2. 426X -X -CV-H4 1.1 180. 2. 427X -X -CQ-H5 1.1 180. 2. 428X -X -CK-H5 1.1 180. 2. 429X -X -CM-H4 1.1 180. 2. 430X -X -CM-HA 1.1 180. 2. 431X -X -CA-H4 1.1 180. 2. bsd.on C6H6 nmodes 432X -X -CA-H5 1.1 180. 2. bsd.on C6H6 nmodes 433CK-CB-N*-CT 1.0 180. 2. 434CM-C -N*-CT 1.0 180. 2. dac guess, 9/94 435CM-C -CM-CT 1.1 180. 2. 436CT-O -C -OH 10.5 180. 2. 437NA-CV-CC-CT 1.1 180. 2. 438NB-CW-CC-CT 1.1 180. 2. 439NA-CW-CC-CT 1.1 180. 2. 440CW-CB-C*-CT 1.1 180. 2. 441CA-CA-CA-CT 1.1 180. 2. 442C -CM-CM-CT 1.1 180. 2. dac guess, 9/94 443NC-CM-CA-N2 1.1 180. 2. dac guess, 9/94 444CB-NC-CA-N2 1.1 180. 2. dac, 10/94 445NA-NC-CA-N2 1.1 180. 2. dac, 10/94 446CA-CA-C -OH 1.1 180. 2. 447 448 HW OW 0000. 0000. 4. flag for fast water 449 450N NA N2 N* NC NB N3 NP NO 451C C* CA CB CC CN CM CK CQ CW CV CR CA CX CY CD 452 453MOD4 RE 454 H 0.6000 0.0157 !Ferguson base pair geom. 455 HO 0.0000 0.0000 OPLS Jorgensen, JACS,110,(1988),1657 456 HS 0.6000 0.0157 W. Cornell CH3SH --> CH3OH FEP 457 HC 1.4870 0.0157 OPLS 458 H1 1.3870 0.0157 Veenstra et al JCC,8,(1992),963 459 H2 1.2870 0.0157 Veenstra et al JCC,8,(1992),963 460 H3 1.1870 0.0157 Veenstra et al JCC,8,(1992),963 461 HP 1.1000 0.0157 Veenstra et al JCC,8,(1992),963 462 HA 1.4590 0.0150 Spellmeyer 463 H4 1.4090 0.0150 Spellmeyer, one electrowithdr. neighbor 464 H5 1.3590 0.0150 Spellmeyer, two electrowithdr. neighbor 465 HW 0.0000 0.0000 TIP3P water model 466 O 1.6612 0.2100 OPLS 467 O2 1.6612 0.2100 OPLS 468 OW 1.7683 0.1520 TIP3P water model 469 OH 1.7210 0.2104 OPLS 470 OS 1.6837 0.1700 OPLS ether 471 CT 1.9080 0.1094 Spellmeyer 472 CA 1.9080 0.0860 Spellmeyer 473 CM 1.9080 0.0860 Spellmeyer 474 C 1.9080 0.0860 OPLS 475 N 1.8240 0.1700 OPLS 476 S 2.0000 0.2500 W. Cornell CH3SH and CH3SCH3 FEP's 477 SH 2.0000 0.2500 W. Cornell CH3SH and CH3SCH3 FEP's 478 P 2.1000 0.2000 JCC,7,(1986),230; 479 IM 2.47 0.1 Cl- Smith & Dang, JCP 1994,100:5,3757 480 Li 1.1370 0.0183 Li+ Aqvist JPC 1990,94,8021. (adapted) 481 IP 1.8680 0.00277 Na+ Aqvist JPC 1990,94,8021. (adapted) 482 K 2.6580 0.000328 K+ Aqvist JPC 1990,94,8021. (adapted) 483 Rb 2.9560 0.00017 Rb+ Aqvist JPC 1990,94,8021. (adapted) 484 Cs 3.3950 0.0000806 Cs+ Aqvist JPC 1990,94,8021. (adapted) 485 I 2.35 0.40 JCC,7,(1986),230; 486 F 1.75 0.061 Gough et al. JCC 13,(1992),963. 487 IB 5.0 0.1 solvated ion for vacuum approximation 488 489END 490END 491 492 493 494# bromine 495TINKER BR 35 1 496TINKER Br 35 1 497# carbon 498TINKER C 6 3 499TINKER CA 6 3 500TINKER CB 6 3 501TINKER CC 6 3 502TINKER CD 6 3 503TINKER CF 6 3 504TINKER CK 6 3 505TINKER CM 6 3 506TINKER CN 6 3 507TINKER CQ 6 3 508TINKER CR 6 3 509TINKER CT 6 4 510TINKER CV 6 3 511TINKER CW 6 3 512TINKER CY 6 2 513TINKER CX 6 2 514TINKER CZ 6 2 515TINKER C5 6 3 516TINKER C* 6 3 517# calcium 518TINKER C0 20 3 519# chloride 520TINKER Cl 17 1 521# fluorine 522TINKER F 9 1 523# hydrogen 524TINKER H 1 1 525TINKER H1 1 1 526TINKER H2 1 1 527TINKER H3 1 1 528TINKER H4 1 1 529TINKER H5 1 1 530TINKER HC 1 1 531TINKER HA 1 1 532TINKER HO 1 1 533TINKER HP 1 1 534TINKER HS 1 1 535TINKER HW 1 1 536TINKER HZ 1 1 537# iodine 538TINKER I 53 1 539# chloride anion 540TINKER IM 17 0 541# magnesium 542TINKER MG 12 0 543# sodium cation 544TINKER Na 11 0 545TINKER IP 11 0 546# nitrogen 547TINKER N 7 3 548TINKER N* 7 2 549TINKER N2 7 3 550TINKER N3 7 4 551TINKER NA 7 3 552TINKER NB 7 2 553TINKER NC 7 2 554TINKER NT 7 3 555TINKER NX 7 2 556TINKER NZ 7 3 557TINKER NY 7 1 558# oxygen 559TINKER O 8 1 560TINKER O2 8 1 561TINKER OW 8 2 562TINKER OH 8 2 563TINKER OS 8 2 564TINKER OM 8 1 565TINKER OZ 8 1 566# phosphate 567TINKER P 15 4 568# sulfter 569TINKER S 16 2 570TINKER SO 16 4 571TINKER SX 16 2 572TINKER SH 16 2 573# copper 574TINKER CU 29 0 575# iron 576TINKER FE 26 0 577# lithium 578TINKER Li 3 0 579# potassium 580TINKER K 19 0 581# rubidium 582TINKER Rb 37 0 583# cesium 584TINKER Cs 55 0 585# calcium (alternate) 586TINKER Ca 20 0 587# dummy 588TINKER X 6 1 589# zinc 590TINKER Z0 30 0 591TINKER Z4 30 4 592TINKER Z5 30 5 593TINKER Zn 30 0 594TINKER LP 0 1 595