; OUT_GMX.top created by acpypi on Mon Oct 26 22:21:30 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 cc cc 0.00000 0.00000 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 cd cd 0.00000 0.00000 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 c2 c2 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 cc_pert cc 0.0000 0.0000 A 3.39967e-01 0.00000e+00 ; perturbed cd_pert cd 0.0000 0.0000 A 3.39967e-01 0.00000e+00 ; perturbed c2_pert c2 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 ] cc cc 1 0.339967 0.359824 cc_pert cc_pert 1 0.339967 0.359824 cc cd 1 0.339967 0.359824 cc_pert cd_pert 1 0.339967 0.359824 cc c2 1 0.339967 0.359824 cc_pert c2_pert 1 0.339967 0.359824 cc nh 1 0.3324835 0.505900795334 cc_pert nh_pert 1 0.3324835 0.505900795334 cc ha 1 0.2999655 0.150274928847 cc_pert ha_pert 1 0.2999655 0.150274928847 cc hn 1 0.2234375 0.153741363241 cc_pert hn_pert 1 0.2234375 0.153741363241 cd cd 1 0.339967 0.359824 cd_pert cd_pert 1 0.339967 0.359824 cd c2 1 0.339967 0.359824 cd_pert c2_pert 1 0.339967 0.359824 cd nh 1 0.3324835 0.505900795334 cd_pert nh_pert 1 0.3324835 0.505900795334 cd ha 1 0.2999655 0.150274928847 cd_pert ha_pert 1 0.2999655 0.150274928847 cd hn 1 0.2234375 0.153741363241 cd_pert hn_pert 1 0.2234375 0.153741363241 c2 c2 1 0.339967 0.359824 c2_pert c2_pert 1 0.339967 0.359824 c2 nh 1 0.3324835 0.505900795334 c2_pert nh_pert 1 0.3324835 0.505900795334 c2 ha 1 0.2999655 0.150274928847 c2_pert ha_pert 1 0.2999655 0.150274928847 c2 hn 1 0.2234375 0.153741363241 c2_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 cc 1 MOL C1 1 -0.01330 12.010000 cc_pert -0.01330 12.010000 ; qtot -0.013 perturbed perturbed 2 cc 1 MOL C2 2 -0.01350 12.010000 cc_pert -0.01350 12.010000 ; qtot -0.027 perturbed perturbed 3 cd 1 MOL C3 3 -0.22490 12.010000 cd_pert -0.22490 12.010000 ; qtot -0.252 perturbed perturbed 4 cd 1 MOL C4 4 -0.22450 12.010000 cd_pert -0.22450 12.010000 ; qtot -0.476 perturbed perturbed 5 cc 1 MOL C5 5 -0.26950 12.010000 cc_pert -0.26950 12.010000 ; qtot -0.746 perturbed perturbed 6 cd 1 MOL C6 6 0.25280 12.010000 cd_pert 0.25280 12.010000 ; qtot -0.493 perturbed perturbed 7 c2 1 MOL C7 7 0.52420 12.010000 c2_pert 0.52420 12.010000 ; qtot 0.031 perturbed perturbed 8 nh 1 MOL N1 8 -0.49740 14.010000 nh_pert -0.49740 14.010000 ; qtot -0.466 perturbed perturbed 9 nh 1 MOL N2 9 -0.82200 14.010000 nh_pert -0.82200 14.010000 ; qtot -1.288 perturbed perturbed 10 nh 1 MOL N3 10 -0.82200 14.010000 nh_pert -0.82200 14.010000 ; qtot -2.110 perturbed perturbed 11 ha 1 MOL H1 11 0.14180 1.008000 ha_pert 0.14180 1.008000 ; qtot -1.968 perturbed perturbed 12 ha 1 MOL H2 12 0.14160 1.008000 ha_pert 0.14160 1.008000 ; qtot -1.827 perturbed perturbed 13 ha 1 MOL H3 13 0.16180 1.008000 ha_pert 0.16180 1.008000 ; qtot -1.665 perturbed perturbed 14 ha 1 MOL H4 14 0.16190 1.008000 ha_pert 0.16190 1.008000 ; qtot -1.503 perturbed perturbed 15 hn 1 MOL H5 15 0.29940 1.008000 hn_pert 0.29940 1.008000 ; qtot -1.204 perturbed perturbed 16 hn 1 MOL H6 16 0.29940 1.008000 hn_pert 0.29940 1.008000 ; qtot -0.904 perturbed perturbed 17 hn 1 MOL H7 17 0.48440 1.008000 hn_pert 0.48440 1.008000 ; qtot -0.420 perturbed perturbed 18 hn 1 MOL H8 18 0.46770 1.008000 hn_pert 0.46770 1.008000 ; qtot 0.048 perturbed perturbed 19 hn 1 MOL H9 19 0.48440 1.008000 hn_pert 0.48440 1.008000 ; qtot 0.532 perturbed perturbed 20 hn 1 MOL H10 20 0.46770 1.008000 hn_pert 0.46770 1.008000 ; qtot 1.000 perturbed perturbed [ bonds ] ; ai aj funct r k 1 3 1 1.3710e-01 4.2175e+05 1.3710e-01 4.2175e+05; C1 - C3 1 5 1 1.4290e-01 3.5003e+05 1.4290e-01 3.5003e+05; C1 - C5 1 11 1 1.0850e-01 2.9054e+05 1.0850e-01 2.9054e+05; C1 - H1 2 4 1 1.3710e-01 4.2175e+05 1.3710e-01 4.2175e+05; C2 - C4 2 5 1 1.4290e-01 3.5003e+05 1.4290e-01 3.5003e+05; C2 - C5 2 12 1 1.0850e-01 2.9054e+05 1.0850e-01 2.9054e+05; C2 - H2 3 6 1 1.4290e-01 3.5003e+05 1.4290e-01 3.5003e+05; C3 - C6 3 13 1 1.0850e-01 2.9054e+05 1.0850e-01 2.9054e+05; C3 - H3 4 6 1 1.4290e-01 3.5003e+05 1.4290e-01 3.5003e+05; C4 - C6 4 14 1 1.0850e-01 2.9054e+05 1.0850e-01 2.9054e+05; C4 - H4 5 7 1 1.3600e-01 4.3731e+05 1.3600e-01 4.3731e+05; C5 - C7 6 8 1 1.3640e-01 3.7572e+05 1.3640e-01 3.7572e+05; C6 - N1 7 9 1 1.3550e-01 3.8710e+05 1.3550e-01 3.8710e+05; C7 - N2 7 10 1 1.3550e-01 3.8710e+05 1.3550e-01 3.8710e+05; C7 - N3 8 15 1 1.0140e-01 3.3572e+05 1.0140e-01 3.3572e+05; N1 - H5 8 16 1 1.0140e-01 3.3572e+05 1.0140e-01 3.3572e+05; N1 - H6 9 17 1 1.0140e-01 3.3572e+05 1.0140e-01 3.3572e+05; N2 - H7 9 18 1 1.0140e-01 3.3572e+05 1.0140e-01 3.3572e+05; N2 - H8 10 19 1 1.0140e-01 3.3572e+05 1.0140e-01 3.3572e+05; N3 - H9 10 20 1 1.0140e-01 3.3572e+05 1.0140e-01 3.3572e+05; N3 - H10 [ pairs ] ; ai aj funct 1 4 1 0.339967 0.179912 1 8 1 0.3324835 0.252950397667 1 9 1 0.3324835 0.252950397667 1 10 1 0.3324835 0.252950397667 1 12 1 0.2999655 0.0751374644235 2 3 1 0.339967 0.179912 2 8 1 0.3324835 0.252950397667 2 9 1 0.3324835 0.252950397667 2 10 1 0.3324835 0.252950397667 3 7 1 0.339967 0.179912 3 14 1 0.2999655 0.0751374644235 3 15 1 0.2234375 0.0768706816205 3 16 1 0.2234375 0.0768706816205 4 7 1 0.339967 0.179912 4 13 1 0.2999655 0.0751374644235 4 15 1 0.2234375 0.0768706816205 4 16 1 0.2234375 0.0768706816205 5 6 1 0.339967 0.179912 5 13 1 0.2999655 0.0751374644235 5 14 1 0.2999655 0.0751374644235 5 17 1 0.2234375 0.0768706816205 5 18 1 0.2234375 0.0768706816205 5 19 1 0.2234375 0.0768706816205 5 20 1 0.2234375 0.0768706816205 6 12 1 0.2999655 0.0751374644235 7 12 1 0.2999655 0.0751374644235 8 13 1 0.292482 0.105640821655 8 14 1 0.292482 0.105640821655 9 19 1 0.215954 0.108077668443 9 20 1 0.215954 0.108077668443 10 17 1 0.215954 0.108077668443 10 18 1 0.215954 0.108077668443 11 2 1 0.2999655 0.0751374644235 11 6 1 0.2999655 0.0751374644235 11 7 1 0.2999655 0.0751374644235 11 13 1 0.259964 0.03138 12 14 1 0.259964 0.03138 [ angles ] ; ai aj ak funct theta cth 1 3 6 1 1.1419e+02 5.7070e+02 1.1419e+02 5.7070e+02; C1 - C3 - C6 1 3 13 1 1.2289e+02 4.0501e+02 1.2289e+02 4.0501e+02; C1 - C3 - H3 1 5 2 1 1.1070e+02 5.6819e+02 1.1070e+02 5.6819e+02; C1 - C5 - C2 1 5 7 1 1.2541e+02 5.4643e+02 1.2541e+02 5.4643e+02; C1 - C5 - C7 2 4 6 1 1.1419e+02 5.7070e+02 1.1419e+02 5.7070e+02; C2 - C4 - C6 2 4 14 1 1.2289e+02 4.0501e+02 1.2289e+02 4.0501e+02; C2 - C4 - H4 2 5 7 1 1.2541e+02 5.4643e+02 1.2541e+02 5.4643e+02; C2 - C5 - C7 3 1 5 1 1.1419e+02 5.7070e+02 1.1419e+02 5.7070e+02; C3 - C1 - C5 3 1 11 1 1.2289e+02 4.0501e+02 1.2289e+02 4.0501e+02; C3 - C1 - H1 3 6 4 1 1.1070e+02 5.6819e+02 1.1070e+02 5.6819e+02; C3 - C6 - C4 3 6 8 1 1.1898e+02 5.7404e+02 1.1898e+02 5.7404e+02; C3 - C6 - N1 4 2 5 1 1.1419e+02 5.7070e+02 1.1419e+02 5.7070e+02; C4 - C2 - C5 4 2 12 1 1.2289e+02 4.0501e+02 1.2289e+02 4.0501e+02; C4 - C2 - H2 4 6 8 1 1.1898e+02 5.7404e+02 1.1898e+02 5.7404e+02; C4 - C6 - N1 5 1 11 1 1.2374e+02 3.8995e+02 1.2374e+02 3.8995e+02; C5 - C1 - H1 5 2 12 1 1.2374e+02 3.8995e+02 1.2374e+02 3.8995e+02; C5 - C2 - H2 5 7 9 1 1.2499e+02 5.8409e+02 1.2499e+02 5.8409e+02; C5 - C7 - N2 5 7 10 1 1.2499e+02 5.8409e+02 1.2499e+02 5.8409e+02; C5 - C7 - N3 6 3 13 1 1.2374e+02 3.8995e+02 1.2374e+02 3.8995e+02; C6 - C3 - H3 6 4 14 1 1.2374e+02 3.8995e+02 1.2374e+02 3.8995e+02; C6 - C4 - H4 6 8 15 1 1.1716e+02 4.0920e+02 1.1716e+02 4.0920e+02; C6 - N1 - H5 6 8 16 1 1.1716e+02 4.0920e+02 1.1716e+02 4.0920e+02; C6 - N1 - H6 7 9 17 1 1.1794e+02 4.1003e+02 1.1794e+02 4.1003e+02; C7 - N2 - H7 7 9 18 1 1.1794e+02 4.1003e+02 1.1794e+02 4.1003e+02; C7 - N2 - H8 7 10 19 1 1.1794e+02 4.1003e+02 1.1794e+02 4.1003e+02; C7 - N3 - H9 7 10 20 1 1.1794e+02 4.1003e+02 1.1794e+02 4.1003e+02; C7 - N3 - H10 9 7 10 1 1.1750e+02 6.1003e+02 1.1750e+02 6.1003e+02; N2 - C7 - N3 15 8 16 1 1.1443e+02 3.3556e+02 1.1443e+02 3.3556e+02; H5 - N1 - H6 17 9 18 1 1.1443e+02 3.3556e+02 1.1443e+02 3.3556e+02; H7 - N2 - H8 19 10 20 1 1.1443e+02 3.3556e+02 1.1443e+02 3.3556e+02; H9 - N3 - H10 [ 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 3 6 4 3 33.47200 0.00000 -33.47200 0.00000 0.00000 0.00000 ; C1- C3- C6- C4 1 3 6 8 3 33.47200 0.00000 -33.47200 0.00000 0.00000 0.00000 ; C1- C3- C6- N1 1 5 2 4 3 33.47200 0.00000 -33.47200 0.00000 0.00000 0.00000 ; C1- C5- C2- C4 1 5 2 12 3 33.47200 0.00000 -33.47200 0.00000 0.00000 0.00000 ; C1- C5- C2- H2 1 5 7 9 3 55.64720 0.00000 -55.64720 0.00000 0.00000 0.00000 ; C1- C5- C7- N2 1 5 7 10 3 55.64720 0.00000 -55.64720 0.00000 0.00000 0.00000 ; C1- C5- C7- N3 2 4 6 3 3 33.47200 0.00000 -33.47200 0.00000 0.00000 0.00000 ; C2- C4- C6- C3 2 4 6 8 3 33.47200 0.00000 -33.47200 0.00000 0.00000 0.00000 ; C2- C4- C6- N1 2 5 7 9 3 55.64720 0.00000 -55.64720 0.00000 0.00000 0.00000 ; C2- C5- C7- N2 2 5 7 10 3 55.64720 0.00000 -55.64720 0.00000 0.00000 0.00000 ; C2- C5- C7- N3 3 1 5 2 3 33.47200 0.00000 -33.47200 0.00000 0.00000 0.00000 ; C3- C1- C5- C2 3 1 5 7 3 33.47200 0.00000 -33.47200 0.00000 0.00000 0.00000 ; C3- C1- C5- C7 3 6 4 14 3 33.47200 0.00000 -33.47200 0.00000 0.00000 0.00000 ; C3- C6- C4- H4 3 6 8 15 3 8.78640 0.00000 -8.78640 0.00000 0.00000 0.00000 ; C3- C6- N1- H5 3 6 8 16 3 8.78640 0.00000 -8.78640 0.00000 0.00000 0.00000 ; C3- C6- N1- H6 4 2 5 7 3 33.47200 0.00000 -33.47200 0.00000 0.00000 0.00000 ; C4- C2- C5- C7 4 6 3 13 3 33.47200 0.00000 -33.47200 0.00000 0.00000 0.00000 ; C4- C6- C3- H3 4 6 8 15 3 8.78640 0.00000 -8.78640 0.00000 0.00000 0.00000 ; C4- C6- N1- H5 4 6 8 16 3 8.78640 0.00000 -8.78640 0.00000 0.00000 0.00000 ; C4- C6- N1- H6 5 1 3 6 3 33.47200 0.00000 -33.47200 0.00000 0.00000 0.00000 ; C5- C1- C3- C6 5 1 3 13 3 33.47200 0.00000 -33.47200 0.00000 0.00000 0.00000 ; C5- C1- C3- H3 5 2 4 6 3 33.47200 0.00000 -33.47200 0.00000 0.00000 0.00000 ; C5- C2- C4- C6 5 2 4 14 3 33.47200 0.00000 -33.47200 0.00000 0.00000 0.00000 ; C5- C2- C4- H4 5 7 9 17 3 5.64840 0.00000 -5.64840 0.00000 0.00000 0.00000 ; C5- C7- N2- H7 5 7 9 18 3 5.64840 0.00000 -5.64840 0.00000 0.00000 0.00000 ; C5- C7- N2- H8 5 7 10 19 3 5.64840 0.00000 -5.64840 0.00000 0.00000 0.00000 ; C5- C7- N3- H9 5 7 10 20 3 5.64840 0.00000 -5.64840 0.00000 0.00000 0.00000 ; C5- C7- N3- H10 6 4 2 12 3 33.47200 0.00000 -33.47200 0.00000 0.00000 0.00000 ; C6- C4- C2- H2 7 5 2 12 3 33.47200 0.00000 -33.47200 0.00000 0.00000 0.00000 ; C7- C5- C2- H2 8 6 3 13 3 33.47200 0.00000 -33.47200 0.00000 0.00000 0.00000 ; N1- C6- C3- H3 8 6 4 14 3 33.47200 0.00000 -33.47200 0.00000 0.00000 0.00000 ; N1- C6- C4- H4 9 7 10 19 3 5.64840 0.00000 -5.64840 0.00000 0.00000 0.00000 ; N2- C7- N3- H9 9 7 10 20 3 5.64840 0.00000 -5.64840 0.00000 0.00000 0.00000 ; N2- C7- N3- H10 10 7 9 17 3 5.64840 0.00000 -5.64840 0.00000 0.00000 0.00000 ; N3- C7- N2- H7 10 7 9 18 3 5.64840 0.00000 -5.64840 0.00000 0.00000 0.00000 ; N3- C7- N2- H8 11 1 3 6 3 33.47200 0.00000 -33.47200 0.00000 0.00000 0.00000 ; H1- C1- C3- C6 11 1 3 13 3 33.47200 0.00000 -33.47200 0.00000 0.00000 0.00000 ; H1- C1- C3- H3 11 1 5 2 3 33.47200 0.00000 -33.47200 0.00000 0.00000 0.00000 ; H1- C1- C5- C2 11 1 5 7 3 33.47200 0.00000 -33.47200 0.00000 0.00000 0.00000 ; H1- C1- C5- C7 12 2 4 14 3 33.47200 0.00000 -33.47200 0.00000 0.00000 0.00000 ; H2- C2- C4- H4 [ dihedrals ] ; impropers ; treated as propers in GROMACS to use correct AMBER analytical function ; i j k l func phase kd pn 1 6 3 13 1 180.00 4.60240 2 ; C1- C6- C3- H3 2 6 4 14 1 180.00 4.60240 2 ; C2- C6- C4- H4 3 4 6 8 1 180.00 4.60240 2 ; C3- C4- C6- N1 5 4 2 12 1 180.00 4.60240 2 ; C5- C4- C2- H2 5 9 7 10 1 180.00 4.60240 2 ; C5- N2- C7- N3 6 15 8 16 1 180.00 4.60240 2 ; C6- H5- N1- H6 7 1 5 2 1 180.00 4.60240 2 ; C7- C1- C5- C2 7 17 9 18 1 180.00 4.60240 2 ; C7- H7- N2- H8 7 19 10 20 1 180.00 4.60240 2 ; C7- H9- N3- H10 11 1 3 5 1 180.00 4.60240 2 ; H1- C1- C3- C5 [ system ] OUT in water [ molecules ] ; Compound nmols OUT 1 SOL 755