595 lines
29 KiB
Plaintext
595 lines
29 KiB
Plaintext
PARM96 for DNA, RNA and proteins with TIP3P Water. USE SCEE=1.2 in energy progs
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BR 79.90 ! bromine
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C 12.01 sp2 C carbonyl group
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CA 12.01 sp2 C pure aromatic (benzene)
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CB 12.01 sp2 aromatic C, 5&6 membered ring junction
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CC 12.01 sp2 aromatic C, 5 memb. ring HIS
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CK 12.01 sp2 C 5 memb.ring in purines
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CM 12.01 sp2 C pyrimidines in pos. 5 & 6
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CN 12.01 sp2 C aromatic 5&6 memb.ring junct.(TRP)
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CQ 12.01 sp2 C in 5 mem.ring of purines between 2 N
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CR 12.01 sp2 arom as CQ but in HIS
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CT 12.01 sp3 aliphatic C
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CV 12.01 sp2 arom. 5 memb.ring w/1 N and 1 H (HIS)
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CW 12.01 sp2 arom. 5 memb.ring w/1 N-H and 1 H (HIS)
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C* 12.01 sp2 arom. 5 memb.ring w/1 subst. (TRP)
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C0 40.08 calcium
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F 19.00 fluorine
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H 1.008 H bonded to nitrogen atoms
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HC 1.008 H aliph. bond. to C without electrwd.group
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H1 1.008 H aliph. bond. to C with 1 electrwd. group
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H2 1.008 H aliph. bond. to C with 2 electrwd.groups
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H3 1.008 H aliph. bond. to C with 3 eletrwd.groups
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HA 1.008 H arom. bond. to C without elctrwd. groups
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H4 1.008 H arom. bond. to C with 1 electrwd. group
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H5 1.008 H arom. bond. to C with 2 electrwd. groups
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HO 1.008 hydroxyl group
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HS 1.008 hydrogen bonded to sulphur
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HW 1.008 H in TIP3P water
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HP 1.008 H bonded to C next to positively charged gr
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I 126.9 iodine
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IM 35.45 assumed to be Cl-
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IP 22.99 assumed to be Na+
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IB 131.0 'big ion w/ waters' for vacuum (Na+, 6H2O)
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MG 24.305 magnesium
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N 14.01 sp2 nitrogen in amide groups
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NA 14.01 sp2 N in 5 memb.ring w/H atom (HIS)
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NB 14.01 sp2 N in 5 memb.ring w/LP (HIS,ADE,GUA)
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NC 14.01 sp2 N in 6 memb.ring w/LP (ADE,GUA)
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N2 14.01 sp2 N in amino groups
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N3 14.01 sp3 N for charged amino groups (Lys, etc)
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N* 14.01 sp2 N
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O 16.00 carbonyl group oxygen
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OW 16.00 oxygen in TIP3P water
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OH 16.00 oxygen in hydroxyl group
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OS 16.00 ether and ester oxygen
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O2 16.00 carboxyl and phosphate group oxygen
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P 30.97 phosphate
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S 32.06 sulphur in disulfide linkage
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SH 32.06 sulphur in cystine
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CU 63.55 copper
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FE 55.00 iron
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Li 6.94 lithium
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K 39.10 potassium
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Rb 85.47 rubidium
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Cs 132.91 cesium
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C H HO N NA NB NC N2 NT N2 N3 N* O OH OS P O2
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OW-HW 553.0 0.9572 ! TIP3P water
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HW-HW 553.0 1.5136 TIP3P water
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C -CA 469.0 1.409 JCC,7,(1986),230; TYR
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C -CB 447.0 1.419 JCC,7,(1986),230; GUA
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C -CM 410.0 1.444 JCC,7,(1986),230; THY,URA
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C -CT 317.0 1.522 JCC,7,(1986),230; AA
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C -N* 424.0 1.383 JCC,7,(1986),230; CYT,URA
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C -NA 418.0 1.388 JCC,7,(1986),230; GUA.URA
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C -NC 457.0 1.358 JCC,7,(1986),230; CYT
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C -O 570.0 1.229 JCC,7,(1986),230; AA,CYT,GUA,THY,URA
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C -O2 656.0 1.250 JCC,7,(1986),230; GLU,ASP
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C -OH 450.0 1.364 JCC,7,(1986),230; TYR
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CA-CA 469.0 1.400 JCC,7,(1986),230; BENZENE,PHE,TRP,TYR
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CA-CB 469.0 1.404 JCC,7,(1986),230; ADE,TRP
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CA-CM 427.0 1.433 JCC,7,(1986),230; CYT
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CA-CT 317.0 1.510 JCC,7,(1986),230; PHE,TYR
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CA-HA 367.0 1.080 changed from 340. bsd on C6H6 nmodes; PHE,TRP,TYR
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CA-H4 367.0 1.080 changed from 340. bsd on C6H6 nmodes; no assigned
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CA-N2 481.0 1.340 JCC,7,(1986),230; ARG,CYT,GUA
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CA-NA 427.0 1.381 JCC,7,(1986),230; GUA
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CA-NC 483.0 1.339 JCC,7,(1986),230; ADE,CYT,GUA
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CB-CB 520.0 1.370 JCC,7,(1986),230; ADE,GUA
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CB-N* 436.0 1.374 JCC,7,(1986),230; ADE,GUA
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CB-NB 414.0 1.391 JCC,7,(1986),230; ADE,GUA
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CB-NC 461.0 1.354 JCC,7,(1986),230; ADE,GUA
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CK-H5 367.0 1.080 changed from 340. bsd on C6H6 nmodes; ADE,GUA
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CK-N* 440.0 1.371 JCC,7,(1986),230; ADE,GUA
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CK-NB 529.0 1.304 JCC,7,(1986),230; ADE,GUA
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CM-CM 549.0 1.350 JCC,7,(1986),230; CYT,THY,URA
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CM-CT 317.0 1.510 JCC,7,(1986),230; THY
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CM-HA 367.0 1.080 changed from 340. bsd on C6H6 nmodes; CYT,URA
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CM-H4 367.0 1.080 changed from 340. bsd on C6H6 nmodes; CYT,URA
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CM-H5 367.0 1.080 changed from 340. bsd on C6H6 nmodes; not assigned
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CM-N* 448.0 1.365 JCC,7,(1986),230; CYT,THY,URA
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CQ-H5 367.0 1.080 changed from 340. bsd on C6H6 nmodes; ADE
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CQ-NC 502.0 1.324 JCC,7,(1986),230; ADE
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CT-CT 310.0 1.526 JCC,7,(1986),230; AA, SUGARS
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CT-HC 340.0 1.090 changed from 331 bsd on NMA nmodes; AA, SUGARS
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CT-H1 340.0 1.090 changed from 331 bsd on NMA nmodes; AA, RIBOSE
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CT-H2 340.0 1.090 changed from 331 bsd on NMA nmodes; SUGARS
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CT-H3 340.0 1.090 changed from 331 bsd on NMA nmodes; not assigned
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CT-HP 340.0 1.090 changed from 331; AA-lysine, methyl ammonium cation
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CT-N* 337.0 1.475 JCC,7,(1986),230; ADE,CYT,GUA,THY,URA
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CT-N2 337.0 1.463 JCC,7,(1986),230; ARG
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CT-OH 320.0 1.410 JCC,7,(1986),230; SUGARS
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CT-OS 320.0 1.410 JCC,7,(1986),230; NUCLEIC ACIDS
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H -N2 434.0 1.010 JCC,7,(1986),230; ADE,CYT,GUA,ARG
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H -N* 434.0 1.010 for plain unmethylated bases ADE,CYT,GUA,ARG
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H -NA 434.0 1.010 JCC,7,(1986),230; GUA,URA,HIS
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HO-OH 553.0 0.960 JCC,7,(1986),230; SUGARS,SER,TYR
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HO-OS 553.0 0.960 JCC,7,(1986),230; NUCLEOTIDE ENDS
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O2-P 525.0 1.480 JCC,7,(1986),230; NA PHOSPHATES
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OH-P 230.0 1.610 JCC,7,(1986),230; NA PHOSPHATES
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OS-P 230.0 1.610 JCC,7,(1986),230; NA PHOSPHATES
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C*-HC 367.0 1.080 changed from 340. bsd on C6H6 nmodes, not needed AA
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C -N 490.0 1.335 JCC,7,(1986),230; AA
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C*-CB 388.0 1.459 JCC,7,(1986),230; TRP
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C*-CT 317.0 1.495 JCC,7,(1986),230; TRP
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C*-CW 546.0 1.352 JCC,7,(1986),230; TRP
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CA-CN 469.0 1.400 JCC,7,(1986),230; TRP
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CB-CN 447.0 1.419 JCC,7,(1986),230; TRP
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CC-CT 317.0 1.504 JCC,7,(1986),230; HIS
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CC-CV 512.0 1.375 JCC,7,(1986),230; HIS(delta)
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CC-CW 518.0 1.371 JCC,7,(1986),230; HIS(epsilon)
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CC-NA 422.0 1.385 JCC,7,(1986),230; HIS
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CC-NB 410.0 1.394 JCC,7,(1986),230; HIS
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CN-NA 428.0 1.380 JCC,7,(1986),230; TRP
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CR-H5 367.0 1.080 changed from 340. bsd on C6H6 nmodes;HIS
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CR-NA 477.0 1.343 JCC,7,(1986),230; HIS
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CR-NB 488.0 1.335 JCC,7,(1986),230; HIS
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CT-N 337.0 1.449 JCC,7,(1986),230; AA
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CT-N3 367.0 1.471 JCC,7,(1986),230; LYS
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CT-S 227.0 1.810 changed from 222.0 based on dimethylS nmodes
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CT-SH 237.0 1.810 changed from 222.0 based on methanethiol nmodes
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CV-H4 367.0 1.080 changed from 340. bsd on C6H6 nmodes; HIS
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CV-NB 410.0 1.394 JCC,7,(1986),230; HIS
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CW-H4 367.0 1.080 changed from 340. bsd on C6H6 nmodes;HIS(epsilon,+)
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CW-NA 427.0 1.381 JCC,7,(1986),230; HIS,TRP
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H -N 434.0 1.010 JCC,7,(1986),230; AA
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H -N3 434.0 1.010 JCC,7,(1986),230; LYS
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HS-SH 274.0 1.336 JCC,7,(1986),230; CYS
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S -S 166.0 2.038 JCC,7,(1986),230; CYX (SCHERAGA)
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CT-F 367.0 1.380 JCC,13,(1992),963;CF4; R0=1.332 FOR CHF3
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HW-OW-HW 100. 104.52 TIP3P water
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HW-HW-OW 0. 127.74 (found in crystallographic water with 3 bonds)
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CB-C -NA 70.0 111.30 NA
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CB-C -O 80.0 128.80
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CM-C -NA 70.0 114.10
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CM-C -O 80.0 125.30
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CT-C -O 80.0 120.40
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CT-C -O2 70.0 117.00
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CT-C -OH 70.0 117.00
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N*-C -NA 70.0 115.40
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N*-C -NC 70.0 118.60
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N*-C -O 80.0 120.90
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NA-C -O 80.0 120.60
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NC-C -O 80.0 122.50
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CT-C -N 70.0 116.60 AA general
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N -C -O 80.0 122.90 AA general
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O -C -O 80.0 126.00 AA COO- terminal residues
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O2-C -O2 80.0 126.00 AA GLU (SCH JPC 79,2379)
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O -C -OH 80.0 126.00
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CA-C -CA 63.0 120.00 changed from 85.0 bsd on C6H6 nmodes; AA tyr
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CA-C -OH 70.0 120.00 AA tyr
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C -CA-CA 63.0 120.00 changed from 85.0 bsd on C6H6 nmodes
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CA-CA-CA 63.0 120.00 changed from 85.0 bsd on C6H6 nmodes
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CA-CA-CB 63.0 120.00 changed from 85.0 bsd on C6H6 nmodes
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CA-CA-CT 70.0 120.00
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CA-CA-HA 35.0 120.00
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CA-CA-H4 35.0 120.00
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CB-CA-HA 35.0 120.00
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CB-CA-H4 35.0 120.00
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CB-CA-N2 70.0 123.50
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CB-CA-NC 70.0 117.30
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CM-CA-N2 70.0 120.10
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CM-CA-NC 70.0 121.50
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N2-CA-NA 70.0 116.00
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N2-CA-NC 70.0 119.30
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NA-CA-NC 70.0 123.30
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C -CA-HA 35.0 120.00 AA tyr
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N2-CA-N2 70.0 120.00 AA arg
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CN-CA-HA 35.0 120.00 AA trp
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CA-CA-CN 63.0 120.00 changed from 85.0 bsd on C6H6 nmodes; AA trp
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C -CB-CB 63.0 119.20 changed from 85.0 bsd on C6H6 nmodes; NA gua
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C -CB-NB 70.0 130.00
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CA-CB-CB 63.0 117.30 changed from 85.0 bsd on C6H6 nmodes; NA ade
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CA-CB-NB 70.0 132.40
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CB-CB-N* 70.0 106.20
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CB-CB-NB 70.0 110.40
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CB-CB-NC 70.0 127.70
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N*-CB-NC 70.0 126.20
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C*-CB-CA 63.0 134.90 changed from 85.0 bsd on C6H6 nmodes; AA trp
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C*-CB-CN 63.0 108.80 changed from 85.0 bsd on C6H6 nmodes; AA trp
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CA-CB-CN 63.0 116.20 changed from 85.0 bsd on C6H6 nmodes; AA trp
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H5-CK-N* 35.0 123.05
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H5-CK-NB 35.0 123.05
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N*-CK-NB 70.0 113.90
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C -CM-CM 63.0 120.70 changed from 85.0 bsd on C6H6 nmodes; NA thy
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C -CM-CT 70.0 119.70
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C -CM-HA 35.0 119.70
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C -CM-H4 35.0 119.70
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CA-CM-CM 63.0 117.00 changed from 85.0 bsd on C6H6 nmodes; NA cyt
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CA-CM-HA 35.0 123.30
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CA-CM-H4 35.0 123.30
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CM-CM-CT 70.0 119.70
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CM-CM-HA 35.0 119.70
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CM-CM-H4 35.0 119.70
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CM-CM-N* 70.0 121.20
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H4-CM-N* 35.0 119.10
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H5-CQ-NC 35.0 115.45
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NC-CQ-NC 70.0 129.10
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CM-CT-HC 50.0 109.50 changed based on NMA nmodes
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CT-CT-CT 40.0 109.50
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CT-CT-HC 50.0 109.50 changed based on NMA nmodes
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CT-CT-H1 50.0 109.50 changed based on NMA nmodes
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CT-CT-H2 50.0 109.50 changed based on NMA nmodes
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CT-CT-HP 50.0 109.50 changed based on NMA nmodes
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CT-CT-N* 50.0 109.50
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CT-CT-OH 50.0 109.50
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CT-CT-OS 50.0 109.50
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HC-CT-HC 35.0 109.50
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H1-CT-H1 35.0 109.50
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HP-CT-HP 35.0 109.50 AA lys, ch3nh4+
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H2-CT-N* 50.0 109.50 changed based on NMA nmodes
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H1-CT-N* 50.0 109.50 changed based on NMA nmodes
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H1-CT-OH 50.0 109.50 changed based on NMA nmodes
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H1-CT-OS 50.0 109.50 changed based on NMA nmodes
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H2-CT-OS 50.0 109.50 changed based on NMA nmodes
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N*-CT-OS 50.0 109.50
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H1-CT-N 50.0 109.50 AA general changed based on NMA nmodes
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C -CT-H1 50.0 109.50 AA general changed based on NMA nmodes
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C -CT-HP 50.0 109.50 AA zwitterion changed based on NMA nmodes
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H1-CT-S 50.0 109.50 AA cys changed based on NMA nmodes
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H1-CT-SH 50.0 109.50 AA cyx changed based on NMA nmodes
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CT-CT-S 50.0 114.70 AA cyx (SCHERAGA JPC 79,1428)
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CT-CT-SH 50.0 108.60 AA cys
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H2-CT-H2 35.0 109.50 AA lys
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H1-CT-N2 50.0 109.50 AA arg changed based on NMA nmodes
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HP-CT-N3 50.0 109.50 AA lys, ch3nh3+, changed based on NMA nmodes
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CA-CT-CT 63.0 114.00 AA phe tyr (SCH JPC 79,2379)
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C -CT-HC 50.0 109.50 AA gln changed based on NMA nmodes
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C -CT-N 63.0 110.10 AA general
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CT-CT-N2 80.0 111.20 AA arg (JCP 76, 1439)
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CT-CT-N 80.0 109.70 AA ala, general (JACS 94, 2657)
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C -CT-CT 63.0 111.10 AA general
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CA-CT-HC 50.0 109.50 AA tyr changed based on NMA nmodes
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CT-CT-N3 80.0 111.20 AA lys (JCP 76, 1439)
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CC-CT-CT 63.0 113.10 AA his
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CC-CT-HC 50.0 109.50 AA his changed based on NMA nmodes
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C -CT-N3 80.0 111.20 AA amino terminal residues
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C*-CT-CT 63.0 115.60 AA trp
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C*-CT-HC 50.0 109.50 AA trp changed based on NMA nmodes
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CT-CC-NA 70.0 120.00 AA his
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CT-CC-CV 70.0 120.00 AA his
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CT-CC-NB 70.0 120.00 AA his
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CV-CC-NA 70.0 120.00 AA his
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CW-CC-NA 70.0 120.00 AA his
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CW-CC-NB 70.0 120.00 AA his
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CT-CC-CW 70.0 120.00 AA his
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H5-CR-NA 35.0 120.00 AA his
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H5-CR-NB 35.0 120.00 AA his
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NA-CR-NA 70.0 120.00 AA his
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NA-CR-NB 70.0 120.00 AA his
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CC-CV-H4 35.0 120.00 AA his
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CC-CV-NB 70.0 120.00 AA his
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H4-CV-NB 35.0 120.00 AA his
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CC-CW-H4 35.0 120.00 AA his
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CC-CW-NA 70.0 120.00 AA his
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H4-CW-NA 35.0 120.00 AA his
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C*-CW-H4 35.0 120.00 AA trp
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C*-CW-NA 70.0 108.70 AA trp
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CT-C*-CW 70.0 125.00 AA trp
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CB-C*-CT 70.0 128.60 AA trp
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CB-C*-CW 63.0 106.40 changed from 85.0 bsd on C6H6 nmodes; AA trp
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CA-CN-NA 70.0 132.80 AA trp
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CB-CN-NA 70.0 104.40 AA trp
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CA-CN-CB 63.0 122.70 changed from 85.0 bsd on C6H6 nmodes; AA trp
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C -N -CT 50.0 121.90 AA general
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C -N -H 30.0 120.00 AA general, gln, asn,changed based on NMA nmodes
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CT-N -H 30.0 118.04 AA general, changed based on NMA nmodes
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CT-N -CT 50.0 118.00 AA pro (DETAR JACS 99,1232)
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H -N -H 35.0 120.00 ade,cyt,gua,gln,asn **
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C -N*-CM 70.0 121.60
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C -N*-CT 70.0 117.60
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C -N*-H 30.0 119.20 changed based on NMA nmodes
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CB-N*-CK 70.0 105.40
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CB-N*-CT 70.0 125.80
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CB-N*-H 30.0 125.80 for unmethylated n.a. bases,chngd bsd NMA nmodes
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CK-N*-CT 70.0 128.80
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CK-N*-H 30.0 128.80 for unmethylated n.a. bases,chngd bsd NMA nmodes
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CM-N*-CT 70.0 121.20
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CM-N*-H 30.0 121.20 for unmethylated n.a. bases,chngd bsd NMA nmodes
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CA-N2-H 35.0 120.00
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H -N2-H 35.0 120.00
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CT-N2-H 35.0 118.40 AA arg
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CA-N2-CT 50.0 123.20 AA arg
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CT-N3-H 50.0 109.50 AA lys, changed based on NMA nmodes
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CT-N3-CT 50.0 109.50 AA pro/nt
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H -N3-H 35.0 109.50 AA lys, AA(end)
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C -NA-C 70.0 126.40
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C -NA-CA 70.0 125.20
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C -NA-H 30.0 116.80 changed based on NMA nmodes
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CA-NA-H 30.0 118.00 changed based on NMA nmodes
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CC-NA-CR 70.0 120.00 AA his
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CC-NA-H 30.0 120.00 AA his, changed based on NMA nmodes
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CR-NA-CW 70.0 120.00 AA his
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CR-NA-H 30.0 120.00 AA his, changed based on NMA nmodes
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CW-NA-H 30.0 120.00 AA his, changed based on NMA nmodes
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CN-NA-CW 70.0 111.60 AA trp
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CN-NA-H 30.0 123.10 AA trp, changed based on NMA nmodes
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CB-NB-CK 70.0 103.80
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CC-NB-CR 70.0 117.00 AA his
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CR-NB-CV 70.0 117.00 AA his
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C -NC-CA 70.0 120.50
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CA-NC-CB 70.0 112.20
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CA-NC-CQ 70.0 118.60
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CB-NC-CQ 70.0 111.00
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C -OH-HO 35.0 113.00
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CT-OH-HO 55.0 108.50
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HO-OH-P 45.0 108.50
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CT-OS-CT 60.0 109.50
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CT-OS-P 100.0 120.50
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P -OS-P 100.0 120.50
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O2-P -OH 45.0 108.23
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O2-P -O2 140.0 119.90
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O2-P -OS 100.0 108.23
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OH-P -OS 45.0 102.60
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OS-P -OS 45.0 102.60
|
|
CT-S -CT 62.0 98.90 AA met
|
|
CT-S -S 68.0 103.70 AA cyx (SCHERAGA JPC 79,1428)
|
|
CT-SH-HS 43.0 96.00 changed from 44.0 based on methanethiol nmodes
|
|
HS-SH-HS 35.0 92.07 AA cys
|
|
F -CT-F 77.0 109.10 JCC,13,(1992),963;
|
|
F -CT-H1 35.0 109.50 JCC,13,(1992),963;
|
|
|
|
X -C -CA-X 4 14.50 180.0 2. intrpol.bsd.on C6H6
|
|
X -C -CB-X 4 12.00 180.0 2. intrpol.bsd.on C6H6
|
|
X -C -CM-X 4 8.70 180.0 2. intrpol.bsd.on C6H6
|
|
X -C -N*-X 4 5.80 180.0 2. JCC,7,(1986),230
|
|
X -C -NA-X 4 5.40 180.0 2. JCC,7,(1986),230
|
|
X -C -NC-X 2 8.00 180.0 2. JCC,7,(1986),230
|
|
X -C -OH-X 2 1.80 180.0 2. JCC,7,(1986),230
|
|
X -C -CT-X 4 0.00 0.0 2. JCC,7,(1986),230
|
|
X -CA-CA-X 4 14.50 180.0 2. intrpol.bsd.on C6H6
|
|
X -CA-CB-X 4 14.00 180.0 2. intrpol.bsd.on C6H6
|
|
X -CA-CM-X 4 10.20 180.0 2. intrpol.bsd.on C6H6
|
|
X -CA-CT-X 6 0.00 0.0 2. JCC,7,(1986),230
|
|
X -CA-N2-X 4 9.60 180.0 2. reinterpolated 93'
|
|
X -CA-NA-X 4 6.00 180.0 2. JCC,7,(1986),230
|
|
X -CA-NC-X 2 9.60 180.0 2. JCC,7,(1986),230
|
|
X -CB-CB-X 4 21.80 180.0 2. intrpol.bsd.on C6H6
|
|
X -CB-N*-X 4 6.60 180.0 2. JCC,7,(1986),230
|
|
X -CB-NB-X 2 5.10 180.0 2. JCC,7,(1986),230
|
|
X -CB-NC-X 2 8.30 180.0 2. JCC,7,(1986),230
|
|
X -CK-N*-X 4 6.80 180.0 2. JCC,7,(1986),230
|
|
X -CK-NB-X 2 20.00 180.0 2. JCC,7,(1986),230
|
|
X -CM-CM-X 4 26.60 180.0 2. intrpol.bsd.on C6H6
|
|
X -CM-CT-X 6 0.00 0.0 3. JCC,7,(1986),230
|
|
X -CM-N*-X 4 7.40 180.0 2. JCC,7,(1986),230
|
|
X -CQ-NC-X 2 13.60 180.0 2. JCC,7,(1986),230
|
|
X -CT-CT-X 9 1.40 0.0 3. JCC,7,(1986),230
|
|
X -CT-N -X 6 0.00 0.0 2. JCC,7,(1986),230
|
|
X -CT-N*-X 6 0.00 0.0 2. JCC,7,(1986),230
|
|
X -CT-N2-X 6 0.00 0.0 3. JCC,7,(1986),230
|
|
X -CT-OH-X 3 0.50 0.0 3. JCC,7,(1986),230
|
|
X -CT-OS-X 3 1.15 0.0 3. JCC,7,(1986),230
|
|
X -OH-P -X 3 0.75 0.0 3. JCC,7,(1986),230
|
|
X -OS-P -X 3 0.75 0.0 3. JCC,7,(1986),230
|
|
X -C -N -X 4 10.00 180.0 2. AA|check Wendy?&NMA
|
|
X -CT-N3-X 9 1.40 0.0 3. JCC,7,(1986),230
|
|
X -CT-S -X 3 1.00 0.0 3. JCC,7,(1986),230
|
|
X -CT-SH-X 3 0.75 0.0 3. JCC,7,(1986),230
|
|
X -C*-CB-X 4 6.70 180.0 2. intrpol.bsd.onC6H6aa
|
|
X -C*-CT-X 6 0.00 0.0 2. JCC,7,(1986),230
|
|
X -C*-CW-X 4 26.10 180.0 2. intrpol.bsd.on C6H6
|
|
X -CA-CN-X 4 14.50 180.0 2. reinterpolated 93'
|
|
X -CB-CN-X 4 12.00 180.0 2. reinterpolated 93'
|
|
X -CC-CT-X 6 0.00 0.0 2. JCC,7,(1986),230
|
|
X -CC-CV-X 4 20.60 180.0 2. intrpol.bsd.on C6H6
|
|
X -CC-CW-X 4 21.50 180.0 2. intrpol.bsd.on C6H6
|
|
X -CC-NA-X 4 5.60 180.0 2. JCC,7,(1986),230
|
|
X -CC-NB-X 2 4.80 180.0 2. JCC,7,(1986),230
|
|
X -CN-NA-X 4 6.10 180.0 2. reinterpolated 93'
|
|
X -CR-NA-X 4 9.30 180.0 2. JCC,7,(1986),230
|
|
X -CR-NB-X 2 10.00 180.0 2. JCC,7,(1986),230
|
|
X -CV-NB-X 2 4.80 180.0 2. JCC,7,(1986),230
|
|
X -CW-NA-X 4 6.00 180.0 2. JCC,7,(1986),230
|
|
CT-CT-OS-CT 1 0.383 0.0 -3.
|
|
CT-CT-OS-CT 1 0.1 180.0 2.
|
|
C -N -CT-C 1 0.30 180.0 -2. Kollman et al. 1997
|
|
C -N -CT-C 1 0.85 000.0 1. Kollman et al. 1997
|
|
N -CT-C -N 1 0.30 180.0 -2. Kollman et al. 1997
|
|
N -CT-C -N 1 0.85 000.0 1. Kollman et al. 1997
|
|
CT-CT-N -C 1 0.50 180.0 -4.
|
|
CT-CT-N -C 1 0.15 180.0 -3.
|
|
CT-CT-N -C 1 0.53 0.0 1.
|
|
CT-CT-C -N 1 0.100 0.0 -4.
|
|
CT-CT-C -N 1 0.07 0.0 2.
|
|
H -N -C -O 1 2.50 180.0 -2. JCC,7,(1986),230
|
|
H -N -C -O 1 2.00 0.0 1. J.C.cistrans-NMA DE
|
|
CT-S -S -CT 1 3.50 0.0 -2. JCC,7,(1986),230
|
|
CT-S -S -CT 1 0.60 0.0 3. JCC,7,(1986),230
|
|
OS-CT-CT-OS 1 0.144 0.0 -3. JCC,7,(1986),230
|
|
OS-CT-CT-OS 1 1.00 0.0 2. pucker anal (93')
|
|
OS-CT-CT-OH 1 0.144 0.0 -3. JCC,7,(1986),230
|
|
OS-CT-CT-OH 1 1.00 0.0 2. pucker anal (93')
|
|
OH-CT-CT-OH 1 0.144 0.0 -3. JCC,7,(1986),230
|
|
OH-CT-CT-OH 1 1.00 0.0 2. check glicolWC? puc
|
|
OH-P -OS-CT 1 0.25 0.0 -3. JCC,7,(1986),230
|
|
OH-P -OS-CT 1 1.20 0.0 2. gg> ene.631g*/mp2
|
|
OS-P -OS-CT 1 0.25 0.0 -3. JCC,7,(1986),230
|
|
OS-P -OS-CT 1 1.20 0.0 2. gg> ene.631g*/mp2
|
|
OS-CT-N*-CK 1 0.50 180.0 -2. sugar frag calc (PC)
|
|
OS-CT-N*-CK 1 2.50 0.0 1. sugar frag calc (PC)
|
|
OS-CT-N*-CM 1 0.50 180.0 -2. sugar frag calc (PC)
|
|
OS-CT-N*-CM 1 2.50 0.0 1. sugar frag calc (PC)
|
|
|
|
X -X -C -O 10.5 180. 2. JCC,7,(1986),230
|
|
X -O2-C -O2 10.5 180. 2. JCC,7,(1986),230
|
|
X -X -N -H 1.0 180. 2. JCC,7,(1986),230
|
|
X -X -N2-H 1.0 180. 2. JCC,7,(1986),230
|
|
X -X -NA-H 1.0 180. 2. JCC,7,(1986),230
|
|
X -N2-CA-N2 10.5 180. 2. JCC,7,(1986),230
|
|
X -CT-N -CT 1.0 180. 2. JCC,7,(1986),230
|
|
X -X -CA-HA 1.1 180. 2. bsd.on C6H6 nmodes
|
|
X -X -CW-H4 1.1 180. 2.
|
|
X -X -CR-H5 1.1 180. 2.
|
|
X -X -CV-H4 1.1 180. 2.
|
|
X -X -CQ-H5 1.1 180. 2.
|
|
X -X -CK-H5 1.1 180. 2.
|
|
X -X -CM-H4 1.1 180. 2.
|
|
X -X -CM-HA 1.1 180. 2.
|
|
X -X -CA-H4 1.1 180. 2. bsd.on C6H6 nmodes
|
|
X -X -CA-H5 1.1 180. 2. bsd.on C6H6 nmodes
|
|
CK-CB-N*-CT 1.0 180. 2.
|
|
CM-C -N*-CT 1.0 180. 2. dac guess, 9/94
|
|
CM-C -CM-CT 1.1 180. 2.
|
|
CT-O -C -OH 10.5 180. 2.
|
|
NA-CV-CC-CT 1.1 180. 2.
|
|
NB-CW-CC-CT 1.1 180. 2.
|
|
NA-CW-CC-CT 1.1 180. 2.
|
|
CW-CB-C*-CT 1.1 180. 2.
|
|
CA-CA-CA-CT 1.1 180. 2.
|
|
C -CM-CM-CT 1.1 180. 2. dac guess, 9/94
|
|
NC-CM-CA-N2 1.1 180. 2. dac guess, 9/94
|
|
CB-NC-CA-N2 1.1 180. 2. dac, 10/94
|
|
NA-NC-CA-N2 1.1 180. 2. dac, 10/94
|
|
CA-CA-C -OH 1.1 180. 2.
|
|
|
|
HW OW 0000. 0000. 4. flag for fast water
|
|
|
|
N NA N2 N* NC NB N3 NP NO
|
|
C C* CA CB CC CN CM CK CQ CW CV CR CA CX CY CD
|
|
|
|
MOD4 RE
|
|
H 0.6000 0.0157 !Ferguson base pair geom.
|
|
HO 0.0000 0.0000 OPLS Jorgensen, JACS,110,(1988),1657
|
|
HS 0.6000 0.0157 W. Cornell CH3SH --> CH3OH FEP
|
|
HC 1.4870 0.0157 OPLS
|
|
H1 1.3870 0.0157 Veenstra et al JCC,8,(1992),963
|
|
H2 1.2870 0.0157 Veenstra et al JCC,8,(1992),963
|
|
H3 1.1870 0.0157 Veenstra et al JCC,8,(1992),963
|
|
HP 1.1000 0.0157 Veenstra et al JCC,8,(1992),963
|
|
HA 1.4590 0.0150 Spellmeyer
|
|
H4 1.4090 0.0150 Spellmeyer, one electrowithdr. neighbor
|
|
H5 1.3590 0.0150 Spellmeyer, two electrowithdr. neighbor
|
|
HW 0.0000 0.0000 TIP3P water model
|
|
O 1.6612 0.2100 OPLS
|
|
O2 1.6612 0.2100 OPLS
|
|
OW 1.7683 0.1520 TIP3P water model
|
|
OH 1.7210 0.2104 OPLS
|
|
OS 1.6837 0.1700 OPLS ether
|
|
CT 1.9080 0.1094 Spellmeyer
|
|
CA 1.9080 0.0860 Spellmeyer
|
|
CM 1.9080 0.0860 Spellmeyer
|
|
C 1.9080 0.0860 OPLS
|
|
N 1.8240 0.1700 OPLS
|
|
S 2.0000 0.2500 W. Cornell CH3SH and CH3SCH3 FEP's
|
|
SH 2.0000 0.2500 W. Cornell CH3SH and CH3SCH3 FEP's
|
|
P 2.1000 0.2000 JCC,7,(1986),230;
|
|
IM 2.47 0.1 Cl- Smith & Dang, JCP 1994,100:5,3757
|
|
Li 1.1370 0.0183 Li+ Aqvist JPC 1990,94,8021. (adapted)
|
|
IP 1.8680 0.00277 Na+ Aqvist JPC 1990,94,8021. (adapted)
|
|
K 2.6580 0.000328 K+ Aqvist JPC 1990,94,8021. (adapted)
|
|
Rb 2.9560 0.00017 Rb+ Aqvist JPC 1990,94,8021. (adapted)
|
|
Cs 3.3950 0.0000806 Cs+ Aqvist JPC 1990,94,8021. (adapted)
|
|
I 2.35 0.40 JCC,7,(1986),230;
|
|
F 1.75 0.061 Gough et al. JCC 13,(1992),963.
|
|
IB 5.0 0.1 solvated ion for vacuum approximation
|
|
|
|
END
|
|
END
|
|
|
|
|
|
|
|
# bromine
|
|
TINKER BR 35 1
|
|
TINKER Br 35 1
|
|
# carbon
|
|
TINKER C 6 3
|
|
TINKER CA 6 3
|
|
TINKER CB 6 3
|
|
TINKER CC 6 3
|
|
TINKER CD 6 3
|
|
TINKER CF 6 3
|
|
TINKER CK 6 3
|
|
TINKER CM 6 3
|
|
TINKER CN 6 3
|
|
TINKER CQ 6 3
|
|
TINKER CR 6 3
|
|
TINKER CT 6 4
|
|
TINKER CV 6 3
|
|
TINKER CW 6 3
|
|
TINKER CY 6 2
|
|
TINKER CX 6 2
|
|
TINKER CZ 6 2
|
|
TINKER C5 6 3
|
|
TINKER C* 6 3
|
|
# calcium
|
|
TINKER C0 20 3
|
|
# chloride
|
|
TINKER Cl 17 1
|
|
# fluorine
|
|
TINKER F 9 1
|
|
# hydrogen
|
|
TINKER H 1 1
|
|
TINKER H1 1 1
|
|
TINKER H2 1 1
|
|
TINKER H3 1 1
|
|
TINKER H4 1 1
|
|
TINKER H5 1 1
|
|
TINKER HC 1 1
|
|
TINKER HA 1 1
|
|
TINKER HO 1 1
|
|
TINKER HP 1 1
|
|
TINKER HS 1 1
|
|
TINKER HW 1 1
|
|
TINKER HZ 1 1
|
|
# iodine
|
|
TINKER I 53 1
|
|
# chloride anion
|
|
TINKER IM 17 0
|
|
# magnesium
|
|
TINKER MG 12 0
|
|
# sodium cation
|
|
TINKER Na 11 0
|
|
TINKER IP 11 0
|
|
# nitrogen
|
|
TINKER N 7 3
|
|
TINKER N* 7 2
|
|
TINKER N2 7 3
|
|
TINKER N3 7 4
|
|
TINKER NA 7 3
|
|
TINKER NB 7 2
|
|
TINKER NC 7 2
|
|
TINKER NT 7 3
|
|
TINKER NX 7 2
|
|
TINKER NZ 7 3
|
|
TINKER NY 7 1
|
|
# oxygen
|
|
TINKER O 8 1
|
|
TINKER O2 8 1
|
|
TINKER OW 8 2
|
|
TINKER OH 8 2
|
|
TINKER OS 8 2
|
|
TINKER OM 8 1
|
|
TINKER OZ 8 1
|
|
# phosphate
|
|
TINKER P 15 4
|
|
# sulfter
|
|
TINKER S 16 2
|
|
TINKER SO 16 4
|
|
TINKER SX 16 2
|
|
TINKER SH 16 2
|
|
# copper
|
|
TINKER CU 29 0
|
|
# iron
|
|
TINKER FE 26 0
|
|
# lithium
|
|
TINKER Li 3 0
|
|
# potassium
|
|
TINKER K 19 0
|
|
# rubidium
|
|
TINKER Rb 37 0
|
|
# cesium
|
|
TINKER Cs 55 0
|
|
# calcium (alternate)
|
|
TINKER Ca 20 0
|
|
# dummy
|
|
TINKER X 6 1
|
|
# zinc
|
|
TINKER Z0 30 0
|
|
TINKER Z4 30 4
|
|
TINKER Z5 30 5
|
|
TINKER Zn 30 0
|
|
TINKER LP 0 1
|