; 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 ca_pert ca 0.0000 0.0000 A 3.39967e-01 0.00000e+00 ; perturbed ce_pert ce 0.0000 0.0000 A 3.39967e-01 0.00000e+00 ; perturbed nh_pert nh 0.0000 0.0000 A 3.25000e-01 0.00000e+00 ; perturbed ha_pert ha 0.0000 0.0000 A 2.59964e-01 0.00000e+00 ; perturbed hn_pert hn 0.0000 0.0000 A 1.06908e-01 0.00000e+00 ; perturbed [ nonbond_params ] ca ca 1 0.339967 0.359824 ca_pert ca_pert 1 0.339967 0.359824 ca ce 1 0.339967 0.359824 ca_pert ce_pert 1 0.339967 0.359824 ca nh 1 0.3324835 0.505900795334 ca_pert nh_pert 1 0.3324835 0.505900795334 ca ha 1 0.2999655 0.150274928847 ca_pert ha_pert 1 0.2999655 0.150274928847 ca hn 1 0.2234375 0.153741363241 ca_pert hn_pert 1 0.2234375 0.153741363241 ce ce 1 0.339967 0.359824 ce_pert ce_pert 1 0.339967 0.359824 ce nh 1 0.3324835 0.505900795334 ce_pert nh_pert 1 0.3324835 0.505900795334 ce ha 1 0.2999655 0.150274928847 ce_pert ha_pert 1 0.2999655 0.150274928847 ce hn 1 0.2234375 0.153741363241 ce_pert hn_pert 1 0.2234375 0.153741363241 nh nh 1 0.325 0.71128 nh_pert nh_pert 1 0.325 0.71128 nh ha 1 0.292482 0.211281643311 nh_pert ha_pert 1 0.292482 0.211281643311 nh hn 1 0.215954 0.216155336885 nh_pert hn_pert 1 0.215954 0.216155336885 ha ha 1 0.259964 0.06276 ha_pert ha_pert 1 0.259964 0.06276 ha hn 1 0.183436 0.0642077027155 ha_pert hn_pert 1 0.183436 0.0642077027155 hn hn 1 0.106908 0.0656888 hn_pert hn_pert 1 0.106908 0.0656888 [ 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_pert -0.05790 12.010000 ; qtot -0.058 perturbed perturbed 2 ca 1 MOL C2 2 -0.11570 12.010000 ca_pert -0.11570 12.010000 ; qtot -0.174 perturbed perturbed 3 ca 1 MOL C3 3 -0.11580 12.010000 ca_pert -0.11580 12.010000 ; qtot -0.289 perturbed perturbed 4 ca 1 MOL C4 4 -0.08240 12.010000 ca_pert -0.08240 12.010000 ; qtot -0.372 perturbed perturbed 5 ca 1 MOL C5 5 -0.08250 12.010000 ca_pert -0.08250 12.010000 ; qtot -0.454 perturbed perturbed 6 ca 1 MOL C6 6 -0.26140 12.010000 ca_pert -0.26140 12.010000 ; qtot -0.716 perturbed perturbed 7 ce 1 MOL C7 7 0.52250 12.010000 ce_pert 0.52250 12.010000 ; qtot -0.193 perturbed perturbed 8 nh 1 MOL N1 8 -0.46900 14.010000 nh_pert -0.46900 14.010000 ; qtot -0.662 perturbed perturbed 9 nh 1 MOL N2 9 -0.45310 14.010000 nh_pert -0.45310 14.010000 ; qtot -1.115 perturbed perturbed 10 ha 1 MOL H1 10 0.17000 1.008000 ha_pert 0.17000 1.008000 ; qtot -0.945 perturbed perturbed 11 ha 1 MOL H2 11 0.16960 1.008000 ha_pert 0.16960 1.008000 ; qtot -0.776 perturbed perturbed 12 ha 1 MOL H3 12 0.16950 1.008000 ha_pert 0.16950 1.008000 ; qtot -0.606 perturbed perturbed 13 ha 1 MOL H4 13 0.14910 1.008000 ha_pert 0.14910 1.008000 ; qtot -0.457 perturbed perturbed 14 ha 1 MOL H5 14 0.14920 1.008000 ha_pert 0.14920 1.008000 ; qtot -0.308 perturbed perturbed 15 hn 1 MOL H6 15 0.33590 1.008000 hn_pert 0.33590 1.008000 ; qtot 0.028 perturbed perturbed 16 hn 1 MOL H7 16 0.31800 1.008000 hn_pert 0.31800 1.008000 ; qtot 0.346 perturbed perturbed 17 hn 1 MOL H8 17 0.33590 1.008000 hn_pert 0.33590 1.008000 ; qtot 0.682 perturbed perturbed 18 hn 1 MOL H9 18 0.31810 1.008000 hn_pert 0.31810 1.008000 ; qtot 1.000 perturbed 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 0.339967 0.179912 1 13 1 0.2999655 0.0751374644235 1 14 1 0.2999655 0.0751374644235 2 5 1 0.339967 0.179912 2 7 1 0.339967 0.179912 2 12 1 0.2999655 0.0751374644235 3 4 1 0.339967 0.179912 3 7 1 0.339967 0.179912 3 11 1 0.2999655 0.0751374644235 4 8 1 0.3324835 0.252950397667 4 9 1 0.3324835 0.252950397667 4 14 1 0.2999655 0.0751374644235 5 8 1 0.3324835 0.252950397667 5 9 1 0.3324835 0.252950397667 5 13 1 0.2999655 0.0751374644235 6 11 1 0.2999655 0.0751374644235 6 12 1 0.2999655 0.0751374644235 6 15 1 0.2234375 0.0768706816205 6 16 1 0.2234375 0.0768706816205 6 17 1 0.2234375 0.0768706816205 6 18 1 0.2234375 0.0768706816205 7 13 1 0.2999655 0.0751374644235 7 14 1 0.2999655 0.0751374644235 8 17 1 0.215954 0.108077668443 8 18 1 0.215954 0.108077668443 9 15 1 0.215954 0.108077668443 9 16 1 0.215954 0.108077668443 10 4 1 0.2999655 0.0751374644235 10 5 1 0.2999655 0.0751374644235 10 11 1 0.259964 0.03138 10 12 1 0.259964 0.03138 11 13 1 0.259964 0.03138 12 14 1 0.259964 0.03138 [ 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