Parmbsc1 force-field for DNA MASS CE 12.001 C1 12.01 0.360 sp2 C purines in pos. 8 Ade (CK) C2 12.01 0.360 sp2 C pyrimidines in pos. 5 & 6 Thy Ura (CM) BOND CE-H1 340.0 1.090 CE-CT 310.0 1.526 OS-CE 320.0 1.410 CE-OH 320.0 1.410 C1-H5 367.0 1.080 changed from 340. bsd on C6H6 nmodes; ADE C1-N* 440.0 1.371 JCC,7,(1986),230; ADE C1-NB 529.0 1.304 JCC,7,(1986),230; ADE C -C2 410.0 1.444 JCC,7,(1986),230; THY,URA C2-C2 549.0 1.350 JCC,7,(1986),230; THY,URA C2-CT 317.0 1.510 JCC,7,(1986),230; THY C2-HA 367.0 1.080 changed from 340. bsd on C6H6 nmodes; CYT,URA C2-H4 367.0 1.080 changed from 340. bsd on C6H6 nmodes; CYT,URA C2-N* 448.0 1.365 JCC,7,(1986),230; CYT,THY,URA ANGLE CT-CE-CT 40.0 109.50 H1-CE-CT 50.0 109.50 H1-CE-OS 50.0 109.50 H1-CT-CE 50.0 109.50 CI-CT-CE 40.0 109.50 CE-CT-OS 50.0 109.50 CE-CT-H1 50.0 109.50 CE-CT-CT 40.0 109.50 CE-CT-HC 50.0 109.50 OS-CE-H1 50.0 109.50 OS-CE-CT 50.0 109.50 P -OS-CE 100.0 120.50 H1-CE-OH 50.0 109.50 CE-OH-HO 55.0 108.50 CT-CE-OH 50.0 109.50 H5-C1-N* 50.0 123.05 H5-C1-NB 50.0 123.05 N*-C1-NB 70.0 113.90 CB-N*-C1 70.0 105.40 C1-N*-CT 70.0 128.80 CB-NB-C1 70.0 103.80 C2-C -NA 70.0 114.10 C2-C -O 80.0 125.30 HC-CT-C2 50.0 109.50 changed based on NMA nmodes C -N*-C2 70.0 121.60 C2-N*-CT 70.0 121.20 C -C2-C2 63.0 120.70 changed from 85.0 bsd on C6H6 nmodes; NA thy C2-C2-CT 70.0 119.70 C2-C2-HA 50.0 119.70 C2-C2-H4 50.0 119.70 C2-C2-N* 70.0 121.20 C -C2-CT 70.0 119.70 C -C2-HA 50.0 119.70 H4-C2-N* 50.0 119.10 DIHEDRAL X -CE-OS-X 3 1.150 0.0 3.0 X -CE-OH-X 3 0.500 0.0 3.0 X -CE-CT-X 9 1.400 0.0 3.0 X -C1-N*-X 4 6.80 180.0 2. JCC,7,(1986),230 X -C1-NB-X 2 20.00 180.0 2. JCC,7,(1986),230 X -C -C2-X 4 8.70 180.0 2. intrpol.bsd.on C6H6 X -C2-C2-X 4 26.60 180.0 2. intrpol.bsd.on C6H6 X -C2-CT-X 6 0.00 0.0 3. JCC,7,(1986),230 X -C2-N*-X 4 7.40 180.0 2. JCC,7,(1986),230 HC-CT-C2-C2 1 0.38 180.0 -3. Junmei et al, 1999 HC-CT-C2-C2 1 1.15 0.0 1. Junmei et al, 1999 C2-C2-C -O 1 2.175 180.0 -2. Junmei et al, 1999 C2-C2-C -O 1 0.30 0.0 3. Junmei et al, 1999 CE-CT-CI-OS 1 1.178040 190.97653 -1.0 gamma CE-CT-CI-OS 1 0.092102 295.63279 -2.0 gamma CE-CT-CI-OS 1 0.962830 348.09535 3.0 gamma CE-CT-CI-OH 1 1.178040 190.97653 -1.0 gamma CE-CT-CI-OH 1 0.092102 295.63279 -2.0 gamma CE-CT-CI-OH 1 0.962830 348.09535 3.0 gamma H1-CI-CT-CE 1 0.160 0.0 3.0 CE-CT-OS-CT 1 0.3833 0.0 -3.0 comes from X -OS-CT-X, parm99.dat CE-CT-OS-CT 1 0.100 180.0 2.0 OS-CE-CT-OS 1 0.144 0.0 -3.0 OS-CE-CT-OS 1 1.175 0.0 2.0 OH-CE-CT-OS 1 0.144 0.0 -3.0 OH-CE-CT-OS 1 1.175 0.0 2.0 P -OS-CE-CT 1 1.079933 297.76503 -1.0 epsilon P -OS-CE-CT 1 0.319017 200.61045 -2.0 epsilon P -OS-CE-CT 1 0.054836 151.62658 3.0 epsilon HO-OH-CE-CT 1 1.079933 297.76503 -1.0 epsilon, 3'term HO-OH-CE-CT 1 0.319017 200.61045 -2.0 epsilon, 3'term HO-OH-CE-CT 1 0.054836 151.62658 3.0 epsilon, 3'term OS- P-OS-CE 1 0.321859 65.91598 -1.0 zeta OS- P-OS-CE 1 0.544600 5.46487 -2.0 zeta OS- P-OS-CE 1 0.797144 295.45281 3.0 zeta CT-CT-CE-CT 1 1.2 38.45 -1.0 puckering CT-CT-CE-CT 1 0.9 -2.23 3.0 puckering CT-CE-CT-OS 1 1.2 322.41 1.0 puckering OS-CT-N*-C1 1 0.41 225.4 -3. bsc1,ade OS-CT-N*-C1 1 1.91 0.7 -2. bsc1,ade OS-CT-N*-C1 1 0.91 120.1 1. bsc1,ade OS-CT-N*-CK 1 0.44 219.8 -3. bsc1,gua OS-CT-N*-CK 1 1.73 4.0 -2. bsc1,gua OS-CT-N*-CK 1 0.81 87.5 1. bsc1,gua OS-CT-N*-C2 1 0.17 210.9 -3. bsc1,ura/thy OS-CT-N*-C2 1 1.67 4.7 -2. bsc1,ura/thy OS-CT-N*-C2 1 0.99 188.0 1. bsc1,ura/thy OS-CT-N*-CM 1 0.26 209.6 -3. bsc1,cyt OS-CT-N*-CM 1 1.52 7.8 -2. bsc1,cyt OS-CT-N*-CM 1 1.03 184.8 1. bsc1,cyt IMPROPER X -X -C1-H5 1.1 180. 2. CB-C1-N*-CT 1.0 180. 2. X -X -C2-H4 1.1 180. 2. X -X -C2-HA 1.1 180. 2. C -C2-N*-CT 1.0 180. 2. dac guess, 9/94 C -C2-C2-CT 1.1 180. 2. dac guess, 9/94 C2-N2-CA-NC 1.1 180. 2. dac guess, 9/94 C2-CT-C2-HA 1.1 180. 2. Junmei et al, 1999 C2-H4-C -O 1.1 180. 2. Junmei et al, 1999 NONBONDED CE 1.9080 0.1094 C1 1.9080 0.0860 Spellmeyer C2 1.9080 0.0860 Spellmeyer