; OUT_GMX.top created by acpypi on Mon Oct 26 22:22:24 2009 #include "ffamber_tip3p.itp [ defaults ] ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ 1 2 yes 0.5 0.8333 [ atomtypes ] ;name bond_type mass charge ptype sigma epsilon Amb ca ca 0.00000 0.00000 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 ce ce 0.00000 0.00000 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 nh nh 0.00000 0.00000 A 3.25000e-01 7.11280e-01 ; 1.82 0.1700 ha ha 0.00000 0.00000 A 2.59964e-01 6.27600e-02 ; 1.46 0.0150 hn hn 0.00000 0.00000 A 1.06908e-01 6.56888e-02 ; 0.60 0.0157 [ moleculetype ] ;name nrexcl OUT 3 [ atoms ] ; nr type resi res atom cgnr charge mass ; qtot bond_type 1 ca 1 MOL C1 1 -0.05790 12.010000 ca 0.00000 12.010000 ; qtot -0.058 perturbed 2 ca 1 MOL C2 2 -0.11570 12.010000 ca 0.00000 12.010000 ; qtot -0.174 perturbed 3 ca 1 MOL C3 3 -0.11580 12.010000 ca 0.00000 12.010000 ; qtot -0.289 perturbed 4 ca 1 MOL C4 4 -0.08240 12.010000 ca 0.00000 12.010000 ; qtot -0.372 perturbed 5 ca 1 MOL C5 5 -0.08250 12.010000 ca 0.00000 12.010000 ; qtot -0.454 perturbed 6 ca 1 MOL C6 6 -0.26140 12.010000 ca 0.00000 12.010000 ; qtot -0.716 perturbed 7 ce 1 MOL C7 7 0.52250 12.010000 ce 0.00000 12.010000 ; qtot -0.193 perturbed 8 nh 1 MOL N1 8 -0.46900 14.010000 nh 0.00000 14.010000 ; qtot -0.662 perturbed 9 nh 1 MOL N2 9 -0.45310 14.010000 nh 0.00000 14.010000 ; qtot -1.115 perturbed 10 ha 1 MOL H1 10 0.17000 1.008000 ha 0.00000 1.008000 ; qtot -0.945 perturbed 11 ha 1 MOL H2 11 0.16960 1.008000 ha 0.00000 1.008000 ; qtot -0.776 perturbed 12 ha 1 MOL H3 12 0.16950 1.008000 ha 0.00000 1.008000 ; qtot -0.606 perturbed 13 ha 1 MOL H4 13 0.14910 1.008000 ha 0.00000 1.008000 ; qtot -0.457 perturbed 14 ha 1 MOL H5 14 0.14920 1.008000 ha 0.00000 1.008000 ; qtot -0.308 perturbed 15 hn 1 MOL H6 15 0.33590 1.008000 hn 0.00000 1.008000 ; qtot 0.028 perturbed 16 hn 1 MOL H7 16 0.31800 1.008000 hn 0.00000 1.008000 ; qtot 0.346 perturbed 17 hn 1 MOL H8 17 0.33590 1.008000 hn 0.00000 1.008000 ; qtot 0.682 perturbed 18 hn 1 MOL H9 18 0.31810 1.008000 hn 0.00000 1.008000 ; qtot 1.000 perturbed [ bonds ] ; ai aj funct r k 1 2 1 1.3870e-01 4.0033e+05 1.3870e-01 4.0033e+05; C1 - C2 1 3 1 1.3870e-01 4.0033e+05 1.3870e-01 4.0033e+05; C1 - C3 1 10 1 1.0870e-01 2.8811e+05 1.0870e-01 2.8811e+05; C1 - H1 2 4 1 1.3870e-01 4.0033e+05 1.3870e-01 4.0033e+05; C2 - C4 2 11 1 1.0870e-01 2.8811e+05 1.0870e-01 2.8811e+05; C2 - H2 3 5 1 1.3870e-01 4.0033e+05 1.3870e-01 4.0033e+05; C3 - C5 3 12 1 1.0870e-01 2.8811e+05 1.0870e-01 2.8811e+05; C3 - H3 4 6 1 1.3870e-01 4.0033e+05 1.3870e-01 4.0033e+05; C4 - C6 4 13 1 1.0870e-01 2.8811e+05 1.0870e-01 2.8811e+05; C4 - H4 5 6 1 1.3870e-01 4.0033e+05 1.3870e-01 4.0033e+05; C5 - C6 5 14 1 1.0870e-01 2.8811e+05 1.0870e-01 2.8811e+05; C5 - H5 6 7 1 1.4720e-01 3.0627e+05 1.4720e-01 3.0627e+05; C6 - C7 7 8 1 1.3410e-01 4.0560e+05 1.3410e-01 4.0560e+05; C7 - N1 7 9 1 1.3410e-01 4.0560e+05 1.3410e-01 4.0560e+05; C7 - N2 8 15 1 1.0140e-01 3.3572e+05 1.0140e-01 3.3572e+05; N1 - H6 8 16 1 1.0140e-01 3.3572e+05 1.0140e-01 3.3572e+05; N1 - H7 9 17 1 1.0140e-01 3.3572e+05 1.0140e-01 3.3572e+05; N2 - H8 9 18 1 1.0140e-01 3.3572e+05 1.0140e-01 3.3572e+05; N2 - H9 [ pairs ] ; ai aj funct 1 6 1 ; C1 - C6 1 13 1 ; C1 - H4 1 14 1 ; C1 - H5 2 5 1 ; C2 - C5 2 7 1 ; C2 - C7 2 12 1 ; C2 - H3 3 4 1 ; C3 - C4 3 7 1 ; C3 - C7 3 11 1 ; C3 - H2 4 8 1 ; C4 - N1 4 9 1 ; C4 - N2 4 14 1 ; C4 - H5 5 8 1 ; C5 - N1 5 9 1 ; C5 - N2 5 13 1 ; C5 - H4 6 11 1 ; C6 - H2 6 12 1 ; C6 - H3 6 15 1 ; C6 - H6 6 16 1 ; C6 - H7 6 17 1 ; C6 - H8 6 18 1 ; C6 - H9 7 13 1 ; C7 - H4 7 14 1 ; C7 - H5 8 17 1 ; N1 - H8 8 18 1 ; N1 - H9 9 15 1 ; N2 - H6 9 16 1 ; N2 - H7 10 4 1 ; H1 - C4 10 5 1 ; H1 - C5 10 11 1 ; H1 - H2 10 12 1 ; H1 - H3 11 13 1 ; H2 - H4 12 14 1 ; H3 - H5 [ angles ] ; ai aj ak funct theta cth 1 2 4 1 1.1997e+02 5.6233e+02 1.1997e+02 5.6233e+02; C1 - C2 - C4 1 2 11 1 1.2001e+02 4.0585e+02 1.2001e+02 4.0585e+02; C1 - C2 - H2 1 3 5 1 1.1997e+02 5.6233e+02 1.1997e+02 5.6233e+02; C1 - C3 - C5 1 3 12 1 1.2001e+02 4.0585e+02 1.2001e+02 4.0585e+02; C1 - C3 - H3 2 1 3 1 1.1997e+02 5.6233e+02 1.1997e+02 5.6233e+02; C2 - C1 - C3 2 1 10 1 1.2001e+02 4.0585e+02 1.2001e+02 4.0585e+02; C2 - C1 - H1 2 4 6 1 1.1997e+02 5.6233e+02 1.1997e+02 5.6233e+02; C2 - C4 - C6 2 4 13 1 1.2001e+02 4.0585e+02 1.2001e+02 4.0585e+02; C2 - C4 - H4 3 1 10 1 1.2001e+02 4.0585e+02 1.2001e+02 4.0585e+02; C3 - C1 - H1 3 5 6 1 1.1997e+02 5.6233e+02 1.1997e+02 5.6233e+02; C3 - C5 - C6 3 5 14 1 1.2001e+02 4.0585e+02 1.2001e+02 4.0585e+02; C3 - C5 - H5 4 2 11 1 1.2001e+02 4.0585e+02 1.2001e+02 4.0585e+02; C4 - C2 - H2 4 6 5 1 1.1997e+02 5.6233e+02 1.1997e+02 5.6233e+02; C4 - C6 - C5 4 6 7 1 1.2066e+02 5.4308e+02 1.2066e+02 5.4308e+02; C4 - C6 - C7 5 3 12 1 1.2001e+02 4.0585e+02 1.2001e+02 4.0585e+02; C5 - C3 - H3 5 6 7 1 1.2066e+02 5.4308e+02 1.2066e+02 5.4308e+02; C5 - C6 - C7 6 4 13 1 1.2001e+02 4.0585e+02 1.2001e+02 4.0585e+02; C6 - C4 - H4 6 5 14 1 1.2001e+02 4.0585e+02 1.2001e+02 4.0585e+02; C6 - C5 - H5 6 7 8 1 1.1769e+02 5.5147e+02 1.1769e+02 5.5147e+02; C6 - C7 - N1 6 7 9 1 1.1769e+02 5.5147e+02 1.1769e+02 5.5147e+02; C6 - C7 - N2 7 8 15 1 1.1473e+02 4.1924e+02 1.1473e+02 4.1924e+02; C7 - N1 - H6 7 8 16 1 1.1473e+02 4.1924e+02 1.1473e+02 4.1924e+02; C7 - N1 - H7 7 9 17 1 1.1473e+02 4.1924e+02 1.1473e+02 4.1924e+02; C7 - N2 - H8 7 9 18 1 1.1473e+02 4.1924e+02 1.1473e+02 4.1924e+02; C7 - N2 - H9 8 7 9 1 1.1750e+02 6.1003e+02 1.1750e+02 6.1003e+02; N1 - C7 - N2 15 8 16 1 1.1443e+02 3.3556e+02 1.1443e+02 3.3556e+02; H6 - N1 - H7 17 9 18 1 1.1443e+02 3.3556e+02 1.1443e+02 3.3556e+02; H8 - N2 - H9 [ dihedrals ] ; propers ; treated as RBs in GROMACS to use combine multiple AMBER torsions per quartet ; i j k l func C0 C1 C2 C3 C4 C5 1 2 4 6 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; C1- C2- C4- C6 1 2 4 13 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; C1- C2- C4- H4 1 3 5 6 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; C1- C3- C5- C6 1 3 5 14 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; C1- C3- C5- H5 2 1 3 5 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; C2- C1- C3- C5 2 1 3 12 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; C2- C1- C3- H3 2 4 6 5 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; C2- C4- C6- C5 2 4 6 7 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; C2- C4- C6- C7 3 1 2 4 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; C3- C1- C2- C4 3 1 2 11 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; C3- C1- C2- H2 3 5 6 4 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; C3- C5- C6- C4 3 5 6 7 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; C3- C5- C6- C7 4 6 5 14 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; C4- C6- C5- H5 4 6 7 8 3 55.64720 0.00000 -55.64720 0.00000 0.00000 0.00000 ; C4- C6- C7- N1 4 6 7 9 3 55.64720 0.00000 -55.64720 0.00000 0.00000 0.00000 ; C4- C6- C7- N2 5 6 4 13 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; C5- C6- C4- H4 5 6 7 8 3 55.64720 0.00000 -55.64720 0.00000 0.00000 0.00000 ; C5- C6- C7- N1 5 6 7 9 3 55.64720 0.00000 -55.64720 0.00000 0.00000 0.00000 ; C5- C6- C7- N2 6 4 2 11 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; C6- C4- C2- H2 6 5 3 12 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; C6- C5- C3- H3 6 7 8 15 3 5.64840 0.00000 -5.64840 0.00000 0.00000 0.00000 ; C6- C7- N1- H6 6 7 8 16 3 5.64840 0.00000 -5.64840 0.00000 0.00000 0.00000 ; C6- C7- N1- H7 6 7 9 17 3 5.64840 0.00000 -5.64840 0.00000 0.00000 0.00000 ; C6- C7- N2- H8 6 7 9 18 3 5.64840 0.00000 -5.64840 0.00000 0.00000 0.00000 ; C6- C7- N2- H9 7 6 4 13 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; C7- C6- C4- H4 7 6 5 14 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; C7- C6- C5- H5 8 7 9 17 3 5.64840 0.00000 -5.64840 0.00000 0.00000 0.00000 ; N1- C7- N2- H8 8 7 9 18 3 5.64840 0.00000 -5.64840 0.00000 0.00000 0.00000 ; N1- C7- N2- H9 9 7 8 15 3 5.64840 0.00000 -5.64840 0.00000 0.00000 0.00000 ; N2- C7- N1- H6 9 7 8 16 3 5.64840 0.00000 -5.64840 0.00000 0.00000 0.00000 ; N2- C7- N1- H7 10 1 2 4 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; H1- C1- C2- C4 10 1 2 11 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; H1- C1- C2- H2 10 1 3 5 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; H1- C1- C3- C5 10 1 3 12 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; H1- C1- C3- H3 11 2 4 13 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; H2- C2- C4- H4 12 3 5 14 3 30.33400 0.00000 -30.33400 0.00000 0.00000 0.00000 ; H3- C3- C5- H5 [ dihedrals ] ; impropers ; treated as propers in GROMACS to use correct AMBER analytical function ; i j k l func phase kd pn 1 4 2 11 1 180.00 4.60240 2 ; C1- C4- C2- H2 1 5 3 12 1 180.00 4.60240 2 ; C1- C5- C3- H3 2 6 4 13 1 180.00 4.60240 2 ; C2- C6- C4- H4 3 6 5 14 1 180.00 4.60240 2 ; C3- C6- C5- H5 4 5 6 7 1 180.00 4.60240 2 ; C4- C5- C6- C7 6 8 7 9 1 180.00 4.60240 2 ; C6- N1- C7- N2 7 15 8 16 1 180.00 4.60240 2 ; C7- H6- N1- H7 7 17 9 18 1 180.00 4.60240 2 ; C7- H8- N2- H9 10 1 3 2 1 180.00 4.60240 2 ; H1- C1- C3- C2 [ system ] OUT in water [ molecules ] ; Compound nmols OUT 1 SOL 689