!BIOSYM forcefield 2 #version amber.frc 1.0 01-May-2000 #define amber > This is the new format version of the amber forcefield !Ver Ref Function Label !---- --- --------------------------------- ------ 1.0 1 atom_types amber 1.0 1 equivalence amber 1.0 1 quadratic_bond amber 1.0 1 quadratic_angle amber 1.0 1 torsion_4 amber 1.0 1 out_of_plane amber 1.0 1 nonbond(12-6) amber #atom_types amber > Atom type definitions for any variant of amber > Masses from CRC 1973/74 pages B-250. !Ver Ref Type Mass Element Comment !---- --- ---- ---------- ------- ----------------------------------------- 1.0 1 BR 79.900000 Br bromine 1.0 1 C 12.010000 C sp2 C carbonyl group 1.0 1 CA 12.010000 C sp2 C pure aromatic (benzene) 1.0 1 CB 12.010000 C sp2 aromatic C, 5&6 membered ring junction 1.0 1 CC 12.010000 C sp2 aromatic C, 5 memb. ring HIS 1.0 1 CK 12.010000 C sp2 C 5 memb.ring in purines 1.0 1 CM 12.010000 C sp2 C pyrimidines in pos. 5 & 6 1.0 1 CN 12.010000 C sp2 C aromatic 5&6 memb.ring junct.(TRP) 1.0 1 CQ 12.010000 C sp2 C in 5 mem.ring of purines between 2 N 1.0 1 CR 12.010000 C sp2 arom as CQ but in HIS 1.0 1 CT 12.010000 C sp3 aliphatic C 1.0 1 CV 12.010000 C sp2 arom. 5 memb.ring w/1 N and 1 H (HIS) 1.0 1 CW 12.010000 C sp2 arom. 5 memb.ring w/1 N-H and 1 H (HIS) 1.0 1 C* 12.010000 C sp2 arom. 5 memb.ring w/1 subst. (TRP) 1.0 1 C0 40.080000 Ca calcium 1.0 1 F 19.000000 F fluorine 1.0 1 H 1.008000 H H bonded to nitrogen atoms 1.0 1 HC 1.008000 H H aliph. bond. to C without electrwd.group 1.0 1 H1 1.008000 H H aliph. bond. to C with 1 electrwd. group 1.0 1 H2 1.008000 H H aliph. bond. to C with 2 electrwd.groups 1.0 1 H3 1.008000 H H aliph. bond. to C with 3 eletrwd.groups 1.0 1 HA 1.008000 H H arom. bond. to C without elctrwd. groups 1.0 1 H4 1.008000 H H arom. bond. to C with 1 electrwd. group 1.0 1 H5 1.008000 H H arom. bond. to C with 2 electrwd. groups 1.0 1 HO 1.008000 H hydroxyl group 1.0 1 HS 1.008000 H hydrogen bonded to sulphur 1.0 1 HW 1.008000 H H in TIP3P water 1.0 1 HP 1.008000 H H bonded to C next to positively charged gr 1.0 1 I 126.900000 I iodine 1.0 1 IM 35.450000 Cl assumed to be Cl- 1.0 1 IP 22.990000 Na assumed to be Na+ 1.0 1 IB 131.000000 IB 'big ion w/ waters' for vacuum (Na+, 6H2O) 1.0 1 MG 24.305000 Mg magnesium 1.0 1 N 14.010000 N sp2 nitrogen in amide groups 1.0 1 NA 14.010000 N sp2 N in 5 memb.ring w/H atom (HIS) 1.0 1 NB 14.010000 N sp2 N in 5 memb.ring w/LP (HIS,ADE,GUA) 1.0 1 NC 14.010000 N sp2 N in 6 memb.ring w/LP (ADE,GUA) 1.0 1 N2 14.010000 N sp2 N in amino groups 1.0 1 N3 14.010000 N sp3 N for charged amino groups (Lys, etc) 1.0 1 N* 14.010000 N sp2 N 1.0 1 O 16.000000 O carbonyl group oxygen 1.0 1 OW 16.000000 O oxygen in TIP3P water 1.0 1 OH 16.000000 O oxygen in hydroxyl group 1.0 1 OS 16.000000 O ether and ester oxygen 1.0 1 O2 16.000000 O carboxyl and phosphate group oxygen 1.0 1 P 30.970000 P phosphate 1.0 1 S 32.060000 S sulphur in disulfide linkage 1.0 1 SH 32.060000 S sulphur in cystine 1.0 1 CU 63.550000 Cu copper 1.0 1 FE 55.000000 Fe iron 1.0 1 Li 6.940000 Li lithium 1.0 1 K 39.100000 K potassium 1.0 1 Rb 85.470000 Rb rubidium 1.0 1 Cs 132.910000 Cs cesium 1.0 1 EP 3.000000 EP "extra point" (mass is ignored) #equivalence amber > Equivalence table for any variant of amber ! Equivalences ! ----------------------------------------- !Ver Ref Type NonB Bond Angle Torsion OOP !---- --- ---- ---- ---- ----- ------- ---- 1.0 1 BR BR BR BR BR BR 1.0 1 C C C C C C 1.0 1 CA CA CA CA CA CA 1.0 1 CB CB CB CB CB CB 1.0 1 CC CC CC CC CC CC 1.0 1 CK CK CK CK CK CK 1.0 1 CM CM CM CM CM CM 1.0 1 CN CN CN CN CN CN 1.0 1 CQ CQ CQ CQ CQ CQ 1.0 1 CR CR CR CR CR CR 1.0 1 CT CT CT CT CT CT 1.0 1 CV CV CV CV CV CV 1.0 1 CW CW CW CW CW CW 1.0 1 C* C* C* C* C* C* 1.0 1 C0 C0 C0 C0 C0 C0 1.0 1 F F F F F F 1.0 1 H H H H H H 1.0 1 HC HC HC HC HC HC 1.0 1 H1 H1 H1 H1 H1 H1 1.0 1 H2 H2 H2 H2 H2 H2 1.0 1 H3 H3 H3 H3 H3 H3 1.0 1 HA HA HA HA HA HA 1.0 1 H4 H4 H4 H4 H4 H4 1.0 1 H5 H5 H5 H5 H5 H5 1.0 1 HO HO HO HO HO HO 1.0 1 HS HS HS HS HS HS 1.0 1 HW HW HW HW HW HW 1.0 1 HP HP HP HP HP HP 1.0 1 I I I I I I 1.0 1 IM IM IM IM IM IM 1.0 1 IP IP IP IP IP IP 1.0 1 IB IB IB IB IB IB 1.0 1 MG MG MG MG MG MG 1.0 1 N N N N N N 1.0 1 NA NA NA NA NA NA 1.0 1 NB NB NB NB NB NB 1.0 1 NC NC NC NC NC NC 1.0 1 N2 N2 N2 N2 N2 N2 1.0 1 N3 N3 N3 N3 N3 N3 1.0 1 N* N* N* N* N* N* 1.0 1 O O O O O O 1.0 1 OW OW OW OW OW OW 1.0 1 OH OH OH OH OH OH 1.0 1 OS OS OS OS OS OS 1.0 1 O2 O2 O2 O2 O2 O2 1.0 1 P P P P P P 1.0 1 S S S S S S 1.0 1 SH SH SH SH SH SH 1.0 1 CU CU CU CU CU CU 1.0 1 FE FE FE FE FE FE 1.0 1 Li Li Li Li Li Li 1.0 1 K K K K K K 1.0 1 Rb Rb Rb Rb Rb Rb 1.0 1 Cs Cs Cs Cs Cs Cs 1.0 1 EP EP EP EP EP EP #quadratic_bond amber > E = K2 * (R - R0)^2 !Ver Ref I J R0 K2 !---- --- ---- ---- ------- -------- 1.0 1 OW HW 0.9572 553.000 1.0 1 HW HW 1.5136 553.000 1.0 1 C CA 1.4090 469.000 1.0 1 C CB 1.4190 447.000 1.0 1 C CM 1.4440 410.000 1.0 1 C CT 1.5220 317.000 1.0 1 C N* 1.3830 424.000 1.0 1 C NA 1.3880 418.000 1.0 1 C NC 1.3580 457.000 1.0 1 C O 1.2290 570.000 1.0 1 C O2 1.2500 656.000 1.0 1 C OH 1.3640 450.000 1.0 1 CA CA 1.4000 469.000 1.0 1 CA CB 1.4040 469.000 1.0 1 CA CM 1.4330 427.000 1.0 1 CA CT 1.5100 317.000 1.0 1 CA HA 1.0800 367.000 1.0 1 CA H4 1.0800 367.000 1.0 1 CA N2 1.3400 481.000 1.0 1 CA NA 1.3810 427.000 1.0 1 CA NC 1.3390 483.000 1.0 1 CB CB 1.3700 520.000 1.0 1 CB N* 1.3740 436.000 1.0 1 CB NB 1.3910 414.000 1.0 1 CB NC 1.3540 461.000 1.0 1 CK H5 1.0800 367.000 1.0 1 CK N* 1.3710 440.000 1.0 1 CK NB 1.3040 529.000 1.0 1 CM CM 1.3500 549.000 1.0 1 CM CT 1.5100 317.000 1.0 1 CM HA 1.0800 367.000 1.0 1 CM H4 1.0800 367.000 1.0 1 CM H5 1.0800 367.000 1.0 1 CM N* 1.3650 448.000 1.0 1 CQ H5 1.0800 367.000 1.0 1 CQ NC 1.3240 502.000 1.0 1 CT CT 1.5260 310.000 1.0 1 CT HC 1.0900 340.000 1.0 1 CT H1 1.0900 340.000 1.0 1 CT H2 1.0900 340.000 1.0 1 CT H3 1.0900 340.000 1.0 1 CT HP 1.0900 340.000 1.0 1 CT N* 1.4750 337.000 1.0 1 CT N2 1.4630 337.000 1.0 1 CT OH 1.4100 320.000 1.0 1 CT OS 1.4100 320.000 1.0 1 H N2 1.0100 434.000 1.0 1 H N* 1.0100 434.000 1.0 1 H NA 1.0100 434.000 1.0 1 HO OH 0.9600 553.000 1.0 1 HO OS 0.9600 553.000 1.0 1 O2 P 1.4800 525.000 1.0 1 OH P 1.6100 230.000 1.0 1 OS P 1.6100 230.000 1.0 1 C* HC 1.0800 367.000 1.0 1 C N 1.3350 490.000 1.0 1 C* CB 1.4590 388.000 1.0 1 C* CT 1.4950 317.000 1.0 1 C* CW 1.3520 546.000 1.0 1 CA CN 1.4000 469.000 1.0 1 CB CN 1.4190 447.000 1.0 1 CC CT 1.5040 317.000 1.0 1 CC CV 1.3750 512.000 1.0 1 CC CW 1.3710 518.000 1.0 1 CC NA 1.3850 422.000 1.0 1 CC NB 1.3940 410.000 1.0 1 CN NA 1.3800 428.000 1.0 1 CR H5 1.0800 367.000 1.0 1 CR NA 1.3430 477.000 1.0 1 CR NB 1.3350 488.000 1.0 1 CT N 1.4490 337.000 1.0 1 CT N3 1.4710 367.000 1.0 1 CT S 1.8100 227.000 1.0 1 CT SH 1.8100 237.000 1.0 1 CV H4 1.0800 367.000 1.0 1 CV NB 1.3940 410.000 1.0 1 CW H4 1.0800 367.000 1.0 1 CW NA 1.3810 427.000 1.0 1 H N 1.0100 434.000 1.0 1 H N3 1.0100 434.000 1.0 1 HS SH 1.3360 274.000 1.0 1 S S 2.0380 166.000 1.0 1 CT F 1.3800 367.000 #quadratic_angle amber > E = K2 * (Theta - Theta0)^2 !Ver Ref I J K Theta0 K2 !---- --- ---- ---- ---- -------- ------- 1.0 1 HW OW HW 104.5200 100.0000 1.0 1 HW HW OW 127.7400 0.0000 1.0 1 CB C NA 111.3000 70.0000 1.0 1 CB C O 128.8000 80.0000 1.0 1 CM C NA 114.1000 70.0000 1.0 1 CM C O 125.3000 80.0000 1.0 1 CT C O 120.4000 80.0000 1.0 1 CT C O2 117.0000 70.0000 1.0 1 CT C OH 117.0000 70.0000 1.0 1 N* C NA 115.4000 70.0000 1.0 1 N* C NC 118.6000 70.0000 1.0 1 N* C O 120.9000 80.0000 1.0 1 NA C O 120.6000 80.0000 1.0 1 NC C O 122.5000 80.0000 1.0 1 CT C N 116.6000 70.0000 1.0 1 N C O 122.9000 80.0000 1.0 1 O C O 126.0000 80.0000 1.0 1 O2 C O2 126.0000 80.0000 1.0 1 O C OH 126.0000 80.0000 1.0 1 CA C CA 120.0000 63.0000 1.0 1 CA C OH 120.0000 70.0000 1.0 1 C CA CA 120.0000 63.0000 1.0 1 CA CA CA 120.0000 63.0000 1.0 1 CA CA CB 120.0000 63.0000 1.0 1 CA CA CT 120.0000 70.0000 1.0 1 CA CA HA 120.0000 35.0000 1.0 1 CA CA H4 120.0000 35.0000 1.0 1 CB CA HA 120.0000 35.0000 1.0 1 CB CA H4 120.0000 35.0000 1.0 1 CB CA N2 123.5000 70.0000 1.0 1 CB CA NC 117.3000 70.0000 1.0 1 CM CA N2 120.1000 70.0000 1.0 1 CM CA NC 121.5000 70.0000 1.0 1 N2 CA NA 116.0000 70.0000 1.0 1 N2 CA NC 119.3000 70.0000 1.0 1 NA CA NC 123.3000 70.0000 1.0 1 C CA HA 120.0000 35.0000 1.0 1 N2 CA N2 120.0000 70.0000 1.0 1 CN CA HA 120.0000 35.0000 1.0 1 CA CA CN 120.0000 63.0000 1.0 1 C CB CB 119.2000 63.0000 1.0 1 C CB NB 130.0000 70.0000 1.0 1 CA CB CB 117.3000 63.0000 1.0 1 CA CB NB 132.4000 70.0000 1.0 1 CB CB N* 106.2000 70.0000 1.0 1 CB CB NB 110.4000 70.0000 1.0 1 CB CB NC 127.7000 70.0000 1.0 1 N* CB NC 126.2000 70.0000 1.0 1 C* CB CA 134.9000 63.0000 1.0 1 C* CB CN 108.8000 63.0000 1.0 1 CA CB CN 116.2000 63.0000 1.0 1 H5 CK N* 123.0500 35.0000 1.0 1 H5 CK NB 123.0500 35.0000 1.0 1 N* CK NB 113.9000 70.0000 1.0 1 C CM CM 120.7000 63.0000 1.0 1 C CM CT 119.7000 70.0000 1.0 1 C CM HA 119.7000 35.0000 1.0 1 C CM H4 119.7000 35.0000 1.0 1 CA CM CM 117.0000 63.0000 1.0 1 CA CM HA 123.3000 35.0000 1.0 1 CA CM H4 123.3000 35.0000 1.0 1 CM CM CT 119.7000 70.0000 1.0 1 CM CM HA 119.7000 35.0000 1.0 1 CM CM H4 119.7000 35.0000 1.0 1 CM CM N* 121.2000 70.0000 1.0 1 H4 CM N* 119.1000 35.0000 1.0 1 H5 CQ NC 115.4500 35.0000 1.0 1 NC CQ NC 129.1000 70.0000 1.0 1 CM CT HC 109.5000 50.0000 1.0 1 CT CT CT 109.5000 40.0000 1.0 1 CT CT HC 109.5000 50.0000 1.0 1 CT CT H1 109.5000 50.0000 1.0 1 CT CT H2 109.5000 50.0000 1.0 1 CT CT HP 109.5000 50.0000 1.0 1 CT CT N* 109.5000 50.0000 1.0 1 CT CT OH 109.5000 50.0000 1.0 1 CT CT OS 109.5000 50.0000 1.0 1 HC CT HC 109.5000 35.0000 1.0 1 H1 CT H1 109.5000 35.0000 1.0 1 HP CT HP 109.5000 35.0000 1.0 1 H2 CT N* 109.5000 50.0000 1.0 1 H1 CT N* 109.5000 50.0000 1.0 1 H1 CT OH 109.5000 50.0000 1.0 1 H1 CT OS 109.5000 50.0000 1.0 1 H2 CT OS 109.5000 50.0000 1.0 1 N* CT OS 109.5000 50.0000 1.0 1 H1 CT N 109.5000 50.0000 1.0 1 C CT H1 109.5000 50.0000 1.0 1 C CT HP 109.5000 50.0000 1.0 1 H1 CT S 109.5000 50.0000 1.0 1 H1 CT SH 109.5000 50.0000 1.0 1 CT CT S 114.7000 50.0000 1.0 1 CT CT SH 108.6000 50.0000 1.0 1 H2 CT H2 109.5000 35.0000 1.0 1 H1 CT N2 109.5000 50.0000 1.0 1 HP CT N3 109.5000 50.0000 1.0 1 CA CT CT 114.0000 63.0000 1.0 1 C CT HC 109.5000 50.0000 1.0 1 C CT N 110.1000 63.0000 1.0 1 CT CT N2 111.2000 80.0000 1.0 1 CT CT N 109.7000 80.0000 1.0 1 C CT CT 111.1000 63.0000 1.0 1 CA CT HC 109.5000 50.0000 1.0 1 CT CT N3 111.2000 80.0000 1.0 1 CC CT CT 113.1000 63.0000 1.0 1 CC CT HC 109.5000 50.0000 1.0 1 C CT N3 111.2000 80.0000 1.0 1 C* CT CT 115.6000 63.0000 1.0 1 C* CT HC 109.5000 50.0000 1.0 1 CT CC NA 120.0000 70.0000 1.0 1 CT CC CV 120.0000 70.0000 1.0 1 CT CC NB 120.0000 70.0000 1.0 1 CV CC NA 120.0000 70.0000 1.0 1 CW CC NA 120.0000 70.0000 1.0 1 CW CC NB 120.0000 70.0000 1.0 1 CT CC CW 120.0000 70.0000 1.0 1 H5 CR NA 120.0000 35.0000 1.0 1 H5 CR NB 120.0000 35.0000 1.0 1 NA CR NA 120.0000 70.0000 1.0 1 NA CR NB 120.0000 70.0000 1.0 1 CC CV H4 120.0000 35.0000 1.0 1 CC CV NB 120.0000 70.0000 1.0 1 H4 CV NB 120.0000 35.0000 1.0 1 CC CW H4 120.0000 35.0000 1.0 1 CC CW NA 120.0000 70.0000 1.0 1 H4 CW NA 120.0000 35.0000 1.0 1 C* CW H4 120.0000 35.0000 1.0 1 C* CW NA 108.7000 70.0000 1.0 1 CT C* CW 125.0000 70.0000 1.0 1 CB C* CT 128.6000 70.0000 1.0 1 CB C* CW 106.4000 63.0000 1.0 1 CA CN NA 132.8000 70.0000 1.0 1 CB CN NA 104.4000 70.0000 1.0 1 CA CN CB 122.7000 63.0000 1.0 1 C N CT 121.9000 50.0000 1.0 1 C N H 120.0000 30.0000 1.0 1 CT N H 118.0400 30.0000 1.0 1 CT N CT 118.0000 50.0000 1.0 1 H N H 120.0000 35.0000 1.0 1 C N* CM 121.6000 70.0000 1.0 1 C N* CT 117.6000 70.0000 1.0 1 C N* H 119.2000 30.0000 1.0 1 CB N* CK 105.4000 70.0000 1.0 1 CB N* CT 125.8000 70.0000 1.0 1 CB N* H 125.8000 30.0000 1.0 1 CK N* CT 128.8000 70.0000 1.0 1 CK N* H 128.8000 30.0000 1.0 1 CM N* CT 121.2000 70.0000 1.0 1 CM N* H 121.2000 30.0000 1.0 1 CA N2 H 120.0000 35.0000 1.0 1 H N2 H 120.0000 35.0000 1.0 1 CT N2 H 118.4000 35.0000 1.0 1 CA N2 CT 123.2000 50.0000 1.0 1 CT N3 H 109.5000 50.0000 1.0 1 CT N3 CT 109.5000 50.0000 1.0 1 H N3 H 109.5000 35.0000 1.0 1 C NA C 126.4000 70.0000 1.0 1 C NA CA 125.2000 70.0000 1.0 1 C NA H 116.8000 30.0000 1.0 1 CA NA H 118.0000 30.0000 1.0 1 CC NA CR 120.0000 70.0000 1.0 1 CC NA H 120.0000 30.0000 1.0 1 CR NA CW 120.0000 70.0000 1.0 1 CR NA H 120.0000 30.0000 1.0 1 CW NA H 120.0000 30.0000 1.0 1 CN NA CW 111.6000 70.0000 1.0 1 CN NA H 123.1000 30.0000 1.0 1 CB NB CK 103.8000 70.0000 1.0 1 CC NB CR 117.0000 70.0000 1.0 1 CR NB CV 117.0000 70.0000 1.0 1 C NC CA 120.5000 70.0000 1.0 1 CA NC CB 112.2000 70.0000 1.0 1 CA NC CQ 118.6000 70.0000 1.0 1 CB NC CQ 111.0000 70.0000 1.0 1 C OH HO 113.0000 35.0000 1.0 1 CT OH HO 108.5000 55.0000 1.0 1 HO OH P 108.5000 45.0000 1.0 1 CT OS CT 109.5000 60.0000 1.0 1 CT OS P 120.5000 100.0000 1.0 1 P OS P 120.5000 100.0000 1.0 1 O2 P OH 108.2300 45.0000 1.0 1 O2 P O2 119.9000 140.0000 1.0 1 O2 P OS 108.2300 100.0000 1.0 1 OH P OS 102.6000 45.0000 1.0 1 OS P OS 102.6000 45.0000 1.0 1 CT S CT 98.9000 62.0000 1.0 1 CT S S 103.7000 68.0000 1.0 1 CT SH HS 96.0000 43.0000 1.0 1 HS SH HS 92.0700 35.0000 1.0 1 F CT F 109.1000 77.0000 1.0 1 F CT H1 109.5000 35.0000 #torsion_4 amber > E = SUM(n=1,4) { (Vn/m) * [ 1 + cos(n*Phi - Phi0(n)) ] } > m = multiplicity or total number of torsions centered on the same bond. !Ver Ref I J K L V1 Phi0 V2 Phi0 V3 Phi0 V4 Phi0 !---- --- ---- ---- ---- ---- ------- ------ ------- ------ ------- ------ ------- ------ 1.0 1 * C CA * 0.0000 0.00 14.5000 180.00 0.0000 0.00 0.0000 0.00 1.0 1 * C CB * 0.0000 0.00 12.0000 180.00 0.0000 0.00 0.0000 0.00 1.0 1 * C CM * 0.0000 0.00 8.7000 180.00 0.0000 0.00 0.0000 0.00 1.0 1 * C N* * 0.0000 0.00 5.8000 180.00 0.0000 0.00 0.0000 0.00 1.0 1 * C NA * 0.0000 0.00 5.4000 180.00 0.0000 0.00 0.0000 0.00 1.0 1 * C NC * 0.0000 0.00 8.0000 180.00 0.0000 0.00 0.0000 0.00 1.0 1 * C OH * 0.0000 0.00 1.8000 180.00 0.0000 0.00 0.0000 0.00 1.0 1 * C CT * 0.0000 0.00 0.0000 0.00 0.0000 0.00 0.0000 0.00 1.0 1 * CA CA * 0.0000 0.00 14.5000 180.00 0.0000 0.00 0.0000 0.00 1.0 1 * CA CB * 0.0000 0.00 14.0000 180.00 0.0000 0.00 0.0000 0.00 1.0 1 * CA CM * 0.0000 0.00 10.2000 180.00 0.0000 0.00 0.0000 0.00 1.0 1 * CA CT * 0.0000 0.00 0.0000 0.00 0.0000 0.00 0.0000 0.00 1.0 1 * CA N2 * 0.0000 0.00 9.6000 180.00 0.0000 0.00 0.0000 0.00 1.0 1 * CA NA * 0.0000 0.00 6.0000 180.00 0.0000 0.00 0.0000 0.00 1.0 1 * CA NC * 0.0000 0.00 9.6000 180.00 0.0000 0.00 0.0000 0.00 1.0 1 * CB CB * 0.0000 0.00 21.8000 180.00 0.0000 0.00 0.0000 0.00 1.0 1 * CB N* * 0.0000 0.00 6.6000 180.00 0.0000 0.00 0.0000 0.00 1.0 1 * CB NB * 0.0000 0.00 5.1000 180.00 0.0000 0.00 0.0000 0.00 1.0 1 * CB NC * 0.0000 0.00 8.3000 180.00 0.0000 0.00 0.0000 0.00 1.0 1 * CK N* * 0.0000 0.00 6.8000 180.00 0.0000 0.00 0.0000 0.00 1.0 1 * CK NB * 0.0000 0.00 20.0000 180.00 0.0000 0.00 0.0000 0.00 1.0 1 * CM CM * 0.0000 0.00 26.6000 180.00 0.0000 0.00 0.0000 0.00 1.0 1 * CM CT * 0.0000 0.00 0.0000 0.00 0.0000 0.00 0.0000 0.00 1.0 1 * CM N* * 0.0000 0.00 7.4000 180.00 0.0000 0.00 0.0000 0.00 1.0 1 * CQ NC * 0.0000 0.00 13.6000 180.00 0.0000 0.00 0.0000 0.00 1.0 1 * CT CT * 0.0000 0.00 0.0000 0.00 1.4000 0.00 0.0000 0.00 1.0 1 * CT N * 0.0000 0.00 0.0000 0.00 0.0000 0.00 0.0000 0.00 1.0 1 * CT N* * 0.0000 0.00 0.0000 0.00 0.0000 0.00 0.0000 0.00 1.0 1 * CT N2 * 0.0000 0.00 0.0000 0.00 0.0000 0.00 0.0000 0.00 1.0 1 * CT OH * 0.0000 0.00 0.0000 0.00 0.5000 0.00 0.0000 0.00 1.0 1 * CT OS * 0.0000 0.00 0.0000 0.00 1.1500 0.00 0.0000 0.00 1.0 1 * OH P * 0.0000 0.00 0.0000 0.00 0.7500 0.00 0.0000 0.00 1.0 1 * OS P * 0.0000 0.00 0.0000 0.00 0.7500 0.00 0.0000 0.00 1.0 1 * C N * 0.0000 0.00 10.0000 180.00 0.0000 0.00 0.0000 0.00 1.0 1 * CT N3 * 0.0000 0.00 0.0000 0.00 1.4000 0.00 0.0000 0.00 1.0 1 * CT S * 0.0000 0.00 0.0000 0.00 1.0000 0.00 0.0000 0.00 1.0 1 * CT SH * 0.0000 0.00 0.0000 0.00 0.7500 0.00 0.0000 0.00 1.0 1 * C* CB * 0.0000 0.00 6.7000 180.00 0.0000 0.00 0.0000 0.00 1.0 1 * C* CT * 0.0000 0.00 0.0000 0.00 0.0000 0.00 0.0000 0.00 1.0 1 * C* CW * 0.0000 0.00 26.1000 180.00 0.0000 0.00 0.0000 0.00 1.0 1 * CA CN * 0.0000 0.00 14.5000 180.00 0.0000 0.00 0.0000 0.00 1.0 1 * CB CN * 0.0000 0.00 12.0000 180.00 0.0000 0.00 0.0000 0.00 1.0 1 * CC CT * 0.0000 0.00 0.0000 0.00 0.0000 0.00 0.0000 0.00 1.0 1 * CC CV * 0.0000 0.00 20.6000 180.00 0.0000 0.00 0.0000 0.00 1.0 1 * CC CW * 0.0000 0.00 21.5000 180.00 0.0000 0.00 0.0000 0.00 1.0 1 * CC NA * 0.0000 0.00 5.6000 180.00 0.0000 0.00 0.0000 0.00 1.0 1 * CC NB * 0.0000 0.00 4.8000 180.00 0.0000 0.00 0.0000 0.00 1.0 1 * CN NA * 0.0000 0.00 6.1000 180.00 0.0000 0.00 0.0000 0.00 1.0 1 * CR NA * 0.0000 0.00 9.3000 180.00 0.0000 0.00 0.0000 0.00 1.0 1 * CR NB * 0.0000 0.00 10.0000 180.00 0.0000 0.00 0.0000 0.00 1.0 1 * CV NB * 0.0000 0.00 4.8000 180.00 0.0000 0.00 0.0000 0.00 1.0 1 * CW NA * 0.0000 0.00 6.0000 180.00 0.0000 0.00 0.0000 0.00 1.0 1 CT CT OS CT 0.0000 0.00 0.1000 180.00 0.3830 0.00 0.0000 0.00 1.0 1 C N CT C 0.0000 0.00 0.2000 180.00 0.0000 0.00 0.0000 0.00 1.0 1 N CT C N 0.7500 180.00 1.3500 180.00 0.0000 0.00 0.4000 180.00 1.0 1 CT CT N C 0.5300 0.00 0.0000 0.00 0.1500 180.00 0.5000 180.00 1.0 1 CT CT C N 0.0000 0.00 0.0700 0.00 0.0000 0.00 0.1000 0.00 1.0 1 H N C O 2.0000 0.00 2.5000 180.00 0.0000 0.00 0.0000 0.00 1.0 1 CT S S CT 0.0000 0.00 3.5000 0.00 0.6000 0.00 0.0000 0.00 1.0 1 OS CT CT OS 0.0000 0.00 1.0000 0.00 0.1440 0.00 0.0000 0.00 1.0 1 OS CT CT OH 0.0000 0.00 1.0000 0.00 0.1440 0.00 0.0000 0.00 1.0 1 OH CT CT OH 0.0000 0.00 1.0000 0.00 0.1440 0.00 0.0000 0.00 1.0 1 OH P OS CT 0.0000 0.00 1.2000 0.00 0.2500 0.00 0.0000 0.00 1.0 1 OS P OS CT 0.0000 0.00 1.2000 0.00 0.2500 0.00 0.0000 0.00 1.0 1 OS CT N* CK 2.5000 0.00 0.5000 180.00 0.0000 0.00 0.0000 0.00 1.0 1 OS CT N* CM 2.5000 0.00 0.5000 180.00 0.0000 0.00 0.0000 0.00 #out_of_plane amber > E = Kchi * [ 1 + cos(n*Chi - Chi0) ] !Ver Ref I J K L Kchi n Chi0 !---- --- ---- ---- ---- ---- ------- ------ ------- 1.0 1 O C * * 10.5000 2 180.0000 1.0 1 O2 C O2 * 10.5000 2 180.0000 1.0 1 H N * * 1.0000 2 180.0000 1.0 1 H N2 * * 1.0000 2 180.0000 1.0 1 H NA * * 1.0000 2 180.0000 1.0 1 N2 CA N2 * 10.5000 2 180.0000 1.0 1 CT N CT * 1.0000 2 180.0000 1.0 1 HA CA * * 1.1000 2 180.0000 1.0 1 H4 CW * * 1.1000 2 180.0000 1.0 1 H5 CR * * 1.1000 2 180.0000 1.0 1 H4 CV * * 1.1000 2 180.0000 1.0 1 H5 CQ * * 1.1000 2 180.0000 1.0 1 H5 CK * * 1.1000 2 180.0000 1.0 1 H4 CM * * 1.1000 2 180.0000 1.0 1 HA CM * * 1.1000 2 180.0000 1.0 1 H4 CA * * 1.1000 2 180.0000 1.0 1 H5 CA * * 1.1000 2 180.0000 1.0 1 CB N* CK CT 1.0000 2 180.0000 1.0 1 C N* CM CT 1.0000 2 180.0000 1.0 1 C CM CM CT 1.1000 2 180.0000 1.0 1 CT C O OH 10.5000 2 180.0000 1.0 1 CT CC CV NA 1.1000 2 180.0000 1.0 1 CT CC CW NB 1.1000 2 180.0000 1.0 1 CT CC CW NA 1.1000 2 180.0000 1.0 1 CB C* CT CW 1.1000 2 180.0000 1.0 1 CA CA CA CT 1.1000 2 180.0000 1.0 1 C CM CM CT 1.1000 2 180.0000 1.0 1 CM CA N2 NC 1.1000 2 180.0000 1.0 1 CB CA N2 NC 1.1000 2 180.0000 1.0 1 N2 CA NA NC 1.1000 2 180.0000 1.0 1 CA C CA OH 1.1000 2 180.0000 #nonbond(12-6) amber @type r-eps @combination arithmetic > E = EPSij * { (Rij*/Rij)^12 - 2(Rij*/Rij)^6 } > where EPSij = sqrt( EPSi * EPSj) > Rij* = (Ri* + Rj*)/2 !!Ver Ref I Ri* EPSi !---- --- ---- ----------- ----------- 1.0 1 H 1.2000 0.01570 1.0 1 HO 0.0000 0.00000 1.0 1 HS 1.2000 0.01570 1.0 1 HC 2.9740 0.01570 1.0 1 H1 2.7740 0.01570 1.0 1 H2 2.5740 0.01570 1.0 1 H3 2.3740 0.01570 1.0 1 HP 2.2000 0.01570 1.0 1 HA 2.9180 0.01500 1.0 1 H4 2.8180 0.01500 1.0 1 H5 2.7180 0.01500 1.0 1 HW 0.0000 0.00000 1.0 1 O 3.3224 0.21000 1.0 1 O2 3.3224 0.21000 1.0 1 OW 3.5364 0.15210 1.0 1 OH 3.4420 0.21040 1.0 1 OS 3.3674 0.17000 1.0 1 CT 3.8160 0.10940 1.0 1 C 3.8160 0.08600 1.0 1 C* 3.8160 0.08600 1.0 1 CA 3.8160 0.08600 1.0 1 CB 3.8160 0.08600 1.0 1 CC 3.8160 0.08600 1.0 1 CN 3.8160 0.08600 1.0 1 CM 3.8160 0.08600 1.0 1 CK 3.8160 0.08600 1.0 1 CQ 3.8160 0.08600 1.0 1 CW 3.8160 0.08600 1.0 1 CV 3.8160 0.08600 1.0 1 CR 3.8160 0.08600 1.0 1 CD 3.8160 0.08600 1.0 1 N 3.6480 0.17000 1.0 1 NA 3.6480 0.17000 1.0 1 N2 3.6480 0.17000 1.0 1 N* 3.6480 0.17000 1.0 1 NC 3.6480 0.17000 1.0 1 NB 3.6480 0.17000 1.0 1 N3 3.6480 0.17000 1.0 1 S 4.0000 0.25000 1.0 1 SH 4.0000 0.25000 1.0 1 P 4.2000 0.20000 1.0 1 IM 4.9400 0.10000 1.0 1 Li 2.2740 0.01830 1.0 1 IP 3.7360 0.00277 1.0 1 K 5.3160 0.00033 1.0 1 Rb 5.9120 0.00017 1.0 1 Cs 6.7900 0.00008 1.0 1 I 4.7000 0.40000 1.0 1 F 3.5000 0.06100 1.0 1 IB ###### 0.10000 1.0 1 EP 0.0000 0.00000 #reference 1 creation of file @Author AD PC GM FyD @Date 01-May-2000 #end