BONDS ! !V(bond) = Kb(b - b0)**2 ! !Kb: kcal/mole/A**2 !b0: A ! !atom type Kb b0 ! !CA CA 305.000 1.3750 ! from BENZ XXXX CAP CAP 370.000 1.3600 ! from 3CB XXXX CAP HP 340.000 1.0800 ! from 3CB XXXX CAP CC 200.000 1.5000 ! from 3CB XXXX CAP CD 200.000 1.5000 ! from 3CB XXXX CAP CL 200.000 1.5000 ! from 3CB XXXX CC OC 525.000 1.2600 ! from ACET XXXX CD OB 750.000 1.2200 ! from ACEH XXXX CD OH1 230.000 1.4000 ! from ACEH XXXX CL OBL 750.000 1.2200 ! from GLYC XXXX CL OSL 150.000 1.3340 ! from GLYC XXXX CTL2 CTL2 222.500 1.5300 ! from GLYC XXXX CTL2 HAL2 309.000 1.1110 ! from GLYC XXXX CTL2 OSL 340.000 1.4300 ! from GLYC XXXX H OH1 545.000 0.9600 ! from ACEH XXXX ANGLES ! !V(angle) = Ktheta(Theta - Theta0)**2 ! !V(Urey-Bradley) = Kub(S - S0)**2 ! !Ktheta: kcal/mole/rad**2 !Theta0: degrees !Kub: kcal/mole/A**2 (Urey-Bradley) !S0: A ! !atom types Ktheta Theta0 Kub S0 ! !CA CA CA 40.000 120.00 35.00 2.41620 ! from BENZ XXXXX CAP CAP CAP 90.00 122.00 30.00 2.3880 ! from 3CB XXXX !CA CA HP 30.000 120.00 22.00 2.15250 ! from BENZ XXXXX CAP CAP HP 30.00 119.00 22.00 2.15250 ! from 3CB XXXX CAP CAP CC 40.00 119.00 35.00 2.41620 ! from 3CB XXXXX CAP CAP CD 40.00 119.00 35.00 2.41620 ! from 3CB XXXXX CAP CAP CL 40.00 119.00 35.00 2.41620 ! from 3CB XXXXX CAP CC OC 40.00 118.00 50.00 2.38800 ! from 3CB XXXXX CAP CD OB 70.000 125.00 20.00 2.44200 ! from ACEH XXXXX CAP CD OH1 55.000 110.5000 ! from ACEH XXXXX CAP CL OBL 70.000 125.00 20.00 2.44200 ! from GLYC XXXXX CAP CL OSL 55.000 109.00 20.00 2.32600 ! from GLYC XXXXX CD OH1 H 55.000 115.0000 ! from ACEH XXXXX CL OSL CTL2 40.000 109.60 30.00 2.26510 ! from GLYC XXXXX CTL2 CTL2 HAL2 26.500 110.10 22.53 2.17900 ! from GLYC XXXXX CTL2 CTL2 OSL 75.700 110.10 ! from GLYC XXXXX HAL2 CTL2 HAL2 35.500 109.00 5.40 1.80200 ! from GLYC XXXXX HAL2 CTL2 OSL 60.000 109.50 ! from GLYC XXXXX OBL CL OSL 90.000 125.90 160.00 2.25760 ! from GLYC XXXXX OB CD OH1 50.000 123.00 210.00 2.26200 ! from ACEH XXXXX OC CC OC 100.000 124.00 70.00 2.22500 ! from ACET XXXXX DIHEDRALS ! !V(dihedral) = Kchi(1 + cos(n(chi) - delta)) ! !Kchi: kcal/mole !n: multiplicity !delta: degrees ! !atom types Kchi n delta ! !CA CA CA CA 3.1000 2 180.00 ! from BENZ XXXXX CAP CAP CAP CAP 1.2000 2 180.00 ! from 3CB XXXXX CC CAP CAP CAP 3.1000 2 180.00 ! from 3CB XXXXX CD CAP CAP CAP 3.1000 2 180.00 ! from 3CB XXXXX CL CAP CAP CAP 3.1000 2 180.00 ! from 3CB XXXXX OC CC CAP CAP 3.100 2 180.00 ! from 3CB XXXXX OSL CL CAP CAP 3.100 2 180.00 ! from 3CB XXXXX OBL CL CAP CAP 3.100 2 180.00 ! from 3CB XXXXX OH1 CD CAP CAP 3.100 2 180.00 ! from 3CB XXXXX OB CD CAP CAP 3.100 2 180.00 ! from 3CB XXXXX HP CAP CAP CAP 4.2000 2 180.00 ! from 3CB XXXXX HP CAP CAP CC 4.2000 2 180.00 ! from 3CB XXXXX HP CAP CAP CD 4.2000 2 180.00 ! from 3CB XXXXX HP CAP CAP CL 4.2000 2 180.00 ! from 3CB XXXXX !HP CA CA HP 2.4000 2 180.00 ! from BENZ XXXXX HP CAP CAP HP 1.9000 2 180.00 ! from 3CB XXXXX OBL CL OSL CTL2 0.9650 1 180.00 ! from GLYC XXXXX OBL CL OSL CTL2 3.8500 2 180.00 ! from GLYC XXXXX, REPEATED X CD OH1 X 2.0500 2 180.00 ! from ACEH XXXXX X CL OSL X 2.0500 2 180.00 ! from GLYC XXXXX CTL2 CTL2 OSL CL 0.7 1 180.00 ! from GLYC XXXXX X CTL2 OSL X 0.00 3 0.00 ! from GLYC XXXXX X CTL2 CTL2 X 0.200 3 0.00 ! from GLYC XXXXX IMPROPER ! !V(improper) = Kpsi(psi - psi0)**2 ! !Kpsi: kcal/mole/rad**2 !psi0: degrees !note that the second column of numbers (0) is ignored ! !atom types Kpsi psi0 ! OC X X CC 96.0000 0 0.0000 ! from ACET OBL X X CL 100.0000 0 0.0000 ! from GLYC OB X X CD 100.0000 0 0.0000 ! from ACEH NONBONDED nbxmod 5 atom cdiel shift vatom vdistance vswitch - cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5 !adm jr., 5/08/91, suggested cutoff scheme ! !V(Lennard-Jones) = Eps,i,j[(Rmin,i,j/ri,j)**12 - 2(Rmin,i,j/ri,j)**6] ! !epsilon: kcal/mole, Eps,i,j = sqrt(eps,i * eps,j) !Rmin/2: A, Rmin,i,j = Rmin/2,i + Rmin/2,j ! !atom ignored epsilon Rmin/2 ignored eps,1-4 Rmin/2,1-4 ! H 0.000000 -0.046000 0.224500 ! HAL2 0.000000 -0.028000 1.340000 ! HP 0.000000 -0.030000 1.358200 0.000000 -0.030000 1.358200 ! CAP 0.000000 -0.070000 1.992400 ! CC 0.000000 -0.070000 2.000000 ! CD 0.000000 -0.070000 2.000000 ! CL 0.000000 -0.070000 2.000000 ! CTL2 0.000000 -0.056000 2.010000 0.000000 -0.010000 1.900000 ! OC 0.000000 -0.120000 1.700000 ! OB 0.000000 -0.120000 1.700000 0.000000 -0.120000 1.400000 ! OBL 0.000000 -0.120000 1.700000 0.000000 -0.120000 1.400000 ! OH1 0.000000 -0.152100 1.770000 ! OSL 0.000000 -0.152100 1.770000 ! HBOND CUTHB 0.5 ! If you want to do hbond analysis (only), then use ! READ PARAM APPEND CARD ! to append hbond parameters from the file: par_hbond.inp END