; LIG_GMX.top created by acpype (Rev: 0) on Sat Jul 4 09:32:06 2020 [ 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 c3 c3 0.00000 0.00000 A 3.39967e-01 4.57730e-01 ; 1.91 0.1094 n4 n4 0.00000 0.00000 A 3.25000e-01 7.11280e-01 ; 1.82 0.1700 c c 0.00000 0.00000 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 o o 0.00000 0.00000 A 2.95992e-01 8.78640e-01 ; 1.66 0.2100 hx hx 0.00000 0.00000 A 1.95998e-01 6.56888e-02 ; 1.10 0.0157 hc hc 0.00000 0.00000 A 2.64953e-01 6.56888e-02 ; 1.49 0.0157 hn hn 0.00000 0.00000 A 1.06908e-01 6.56888e-02 ; 0.60 0.0157 [ moleculetype ] ;name nrexcl LIG 3 [ atoms ] ; nr type resi res atom cgnr charge mass ; qtot bond_type 1 c3 1 LIG CA 1 -0.025500 12.01000 ; qtot -0.026 2 n4 1 LIG N 2 -0.826601 14.01000 ; qtot -0.852 3 c 1 LIG C 3 0.896600 12.01000 ; qtot 0.044 4 o 1 LIG O 4 -0.794301 16.00000 ; qtot -0.750 5 o 1 LIG OXT 5 -0.794301 16.00000 ; qtot -1.544 6 c3 1 LIG CB 6 -0.088400 12.01000 ; qtot -1.633 7 c3 1 LIG CG 7 -0.097400 12.01000 ; qtot -1.730 8 c3 1 LIG CD 8 -0.105400 12.01000 ; qtot -1.835 9 c3 1 LIG CE 9 0.100800 12.01000 ; qtot -1.735 10 n4 1 LIG NZ 10 -0.848601 14.01000 ; qtot -2.583 11 hx 1 LIG HA 11 0.121700 1.00800 ; qtot -2.461 12 hc 1 LIG HB2 12 0.060200 1.00800 ; qtot -2.401 13 hc 1 LIG HB3 13 0.060200 1.00800 ; qtot -2.341 14 hc 1 LIG HG2 14 0.081700 1.00800 ; qtot -2.259 15 hc 1 LIG HG3 15 0.081700 1.00800 ; qtot -2.178 16 hc 1 LIG HD2 16 0.080200 1.00800 ; qtot -2.097 17 hc 1 LIG HD3 17 0.080200 1.00800 ; qtot -2.017 18 hx 1 LIG HE2 18 0.109700 1.00800 ; qtot -1.908 19 hx 1 LIG HE3 19 0.109700 1.00800 ; qtot -1.798 20 hn 1 LIG HZ1 20 0.473133 1.00800 ; qtot -1.325 21 hn 1 LIG HZ2 21 0.473133 1.00800 ; qtot -0.852 22 hn 1 LIG HZ3 22 0.473133 1.00800 ; qtot -0.378 23 hn 1 LIG H1 23 0.459467 1.00800 ; qtot 0.081 24 hn 1 LIG H2 24 0.459467 1.00800 ; qtot 0.541 25 hn 1 LIG H3 25 0.459467 1.00800 ; qtot 1.000 [ bonds ] ; ai aj funct r k 1 2 1 1.5110e-01 2.3707e+05 ; CA - N 1 3 1 1.5241e-01 2.6192e+05 ; CA - C 1 6 1 1.5375e-01 2.5179e+05 ; CA - CB 1 11 1 1.0910e-01 2.8342e+05 ; CA - HA 2 23 1 1.0304e-01 3.1229e+05 ; N - H1 2 24 1 1.0304e-01 3.1229e+05 ; N - H2 2 25 1 1.0304e-01 3.1229e+05 ; N - H3 3 4 1 1.2183e-01 5.3363e+05 ; C - O 3 5 1 1.2183e-01 5.3363e+05 ; C - OXT 6 7 1 1.5375e-01 2.5179e+05 ; CB - CG 6 12 1 1.0969e-01 2.7665e+05 ; CB - HB2 6 13 1 1.0969e-01 2.7665e+05 ; CB - HB3 7 8 1 1.5375e-01 2.5179e+05 ; CG - CD 7 14 1 1.0969e-01 2.7665e+05 ; CG - HG2 7 15 1 1.0969e-01 2.7665e+05 ; CG - HG3 8 9 1 1.5375e-01 2.5179e+05 ; CD - CE 8 16 1 1.0969e-01 2.7665e+05 ; CD - HD2 8 17 1 1.0969e-01 2.7665e+05 ; CD - HD3 9 10 1 1.5110e-01 2.3707e+05 ; CE - NZ 9 18 1 1.0910e-01 2.8342e+05 ; CE - HE2 9 19 1 1.0910e-01 2.8342e+05 ; CE - HE3 10 20 1 1.0304e-01 3.1229e+05 ; NZ - HZ1 10 21 1 1.0304e-01 3.1229e+05 ; NZ - HZ2 10 22 1 1.0304e-01 3.1229e+05 ; NZ - HZ3 [ pairs ] ; ai aj funct 1 8 1 ; CA - CD 1 14 1 ; CA - HG2 1 15 1 ; CA - HG3 2 4 1 ; N - O 2 5 1 ; N - OXT 2 7 1 ; N - CG 2 12 1 ; N - HB2 2 13 1 ; N - HB3 3 7 1 ; C - CG 3 12 1 ; C - HB2 3 13 1 ; C - HB3 3 23 1 ; C - H1 3 24 1 ; C - H2 3 25 1 ; C - H3 6 4 1 ; CB - O 6 5 1 ; CB - OXT 6 9 1 ; CB - CE 6 16 1 ; CB - HD2 6 17 1 ; CB - HD3 6 23 1 ; CB - H1 6 24 1 ; CB - H2 6 25 1 ; CB - H3 7 10 1 ; CG - NZ 7 18 1 ; CG - HE2 7 19 1 ; CG - HE3 8 12 1 ; CD - HB2 8 13 1 ; CD - HB3 8 20 1 ; CD - HZ1 8 21 1 ; CD - HZ2 8 22 1 ; CD - HZ3 9 14 1 ; CE - HG2 9 15 1 ; CE - HG3 10 16 1 ; NZ - HD2 10 17 1 ; NZ - HD3 11 4 1 ; HA - O 11 5 1 ; HA - OXT 11 7 1 ; HA - CG 11 12 1 ; HA - HB2 11 13 1 ; HA - HB3 11 23 1 ; HA - H1 11 24 1 ; HA - H2 11 25 1 ; HA - H3 12 14 1 ; HB2 - HG2 12 15 1 ; HB2 - HG3 13 14 1 ; HB3 - HG2 13 15 1 ; HB3 - HG3 14 16 1 ; HG2 - HD2 14 17 1 ; HG2 - HD3 15 16 1 ; HG3 - HD2 15 17 1 ; HG3 - HD3 16 18 1 ; HD2 - HE2 16 19 1 ; HD2 - HE3 17 18 1 ; HD3 - HE2 17 19 1 ; HD3 - HE3 18 20 1 ; HE2 - HZ1 18 21 1 ; HE2 - HZ2 18 22 1 ; HE2 - HZ3 19 20 1 ; HE3 - HZ1 19 21 1 ; HE3 - HZ2 19 22 1 ; HE3 - HZ3 [ angles ] ; ai aj ak funct theta cth 1 2 23 1 1.1011e+02 3.8409e+02 ; CA - N - H1 1 2 24 1 1.1011e+02 3.8409e+02 ; CA - N - H2 1 2 25 1 1.1011e+02 3.8409e+02 ; CA - N - H3 1 3 4 1 1.2320e+02 5.6400e+02 ; CA - C - O 1 3 5 1 1.2320e+02 5.6400e+02 ; CA - C - OXT 1 6 7 1 1.1151e+02 5.2635e+02 ; CA - CB - CG 1 6 12 1 1.0980e+02 3.8744e+02 ; CA - CB - HB2 1 6 13 1 1.0980e+02 3.8744e+02 ; CA - CB - HB3 2 1 3 1 1.1073e+02 5.4810e+02 ; N - CA - C 2 1 6 1 1.1421e+02 5.3723e+02 ; N - CA - CB 2 1 11 1 1.0801e+02 4.0668e+02 ; N - CA - HA 3 1 6 1 1.1104e+02 5.2969e+02 ; C - CA - CB 3 1 11 1 1.0885e+02 3.9246e+02 ; C - CA - HA 4 3 5 1 1.3025e+02 6.5187e+02 ; O - C - OXT 6 1 11 1 1.1056e+02 3.8660e+02 ; CB - CA - HA 6 7 8 1 1.1151e+02 5.2635e+02 ; CB - CG - CD 6 7 14 1 1.0980e+02 3.8744e+02 ; CB - CG - HG2 6 7 15 1 1.0980e+02 3.8744e+02 ; CB - CG - HG3 7 6 12 1 1.0980e+02 3.8744e+02 ; CG - CB - HB2 7 6 13 1 1.0980e+02 3.8744e+02 ; CG - CB - HB3 7 8 9 1 1.1151e+02 5.2635e+02 ; CG - CD - CE 7 8 16 1 1.0980e+02 3.8744e+02 ; CG - CD - HD2 7 8 17 1 1.0980e+02 3.8744e+02 ; CG - CD - HD3 8 7 14 1 1.0980e+02 3.8744e+02 ; CD - CG - HG2 8 7 15 1 1.0980e+02 3.8744e+02 ; CD - CG - HG3 8 9 10 1 1.1421e+02 5.3723e+02 ; CD - CE - NZ 8 9 18 1 1.1056e+02 3.8660e+02 ; CD - CE - HE2 8 9 19 1 1.1056e+02 3.8660e+02 ; CD - CE - HE3 9 8 16 1 1.0980e+02 3.8744e+02 ; CE - CD - HD2 9 8 17 1 1.0980e+02 3.8744e+02 ; CE - CD - HD3 9 10 20 1 1.1011e+02 3.8409e+02 ; CE - NZ - HZ1 9 10 21 1 1.1011e+02 3.8409e+02 ; CE - NZ - HZ2 9 10 22 1 1.1011e+02 3.8409e+02 ; CE - NZ - HZ3 10 9 18 1 1.0801e+02 4.0668e+02 ; NZ - CE - HE2 10 9 19 1 1.0801e+02 4.0668e+02 ; NZ - CE - HE3 12 6 13 1 1.0758e+02 3.2970e+02 ; HB2 - CB - HB3 14 7 15 1 1.0758e+02 3.2970e+02 ; HG2 - CG - HG3 16 8 17 1 1.0758e+02 3.2970e+02 ; HD2 - CD - HD3 18 9 19 1 1.0975e+02 3.2803e+02 ; HE2 - CE - HE3 20 10 21 1 1.0830e+02 3.3974e+02 ; HZ1 - NZ - HZ2 20 10 22 1 1.0830e+02 3.3974e+02 ; HZ1 - NZ - HZ3 21 10 22 1 1.0830e+02 3.3974e+02 ; HZ2 - NZ - HZ3 23 2 24 1 1.0830e+02 3.3974e+02 ; H1 - N - H2 23 2 25 1 1.0830e+02 3.3974e+02 ; H1 - N - H3 24 2 25 1 1.0830e+02 3.3974e+02 ; H2 - N - H3 [ 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 6 7 8 3 3.68192 3.09616 -2.09200 -3.01248 0.00000 0.00000 ; CA- CB- CG- CD 1 6 7 14 3 0.66944 2.00832 0.00000 -2.67776 0.00000 0.00000 ; CA- CB- CG- HG2 1 6 7 15 3 0.66944 2.00832 0.00000 -2.67776 0.00000 0.00000 ; CA- CB- CG- HG3 2 1 3 4 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; N- CA- C- O 2 1 3 5 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; N- CA- C- OXT 2 1 6 7 3 0.65084 1.95253 0.00000 -2.60338 0.00000 0.00000 ; N- CA- CB- CG 2 1 6 12 3 0.65084 1.95253 0.00000 -2.60338 0.00000 0.00000 ; N- CA- CB- HB2 2 1 6 13 3 0.65084 1.95253 0.00000 -2.60338 0.00000 0.00000 ; N- CA- CB- HB3 3 1 2 23 3 0.65084 1.95253 0.00000 -2.60338 0.00000 0.00000 ; C- CA- N- H1 3 1 2 24 3 0.65084 1.95253 0.00000 -2.60338 0.00000 0.00000 ; C- CA- N- H2 3 1 2 25 3 0.65084 1.95253 0.00000 -2.60338 0.00000 0.00000 ; C- CA- N- H3 3 1 6 7 3 0.65084 1.95253 0.00000 -2.60338 0.00000 0.00000 ; C- CA- CB- CG 3 1 6 12 3 0.65084 1.95253 0.00000 -2.60338 0.00000 0.00000 ; C- CA- CB- HB2 3 1 6 13 3 0.65084 1.95253 0.00000 -2.60338 0.00000 0.00000 ; C- CA- CB- HB3 6 1 2 23 3 0.65084 1.95253 0.00000 -2.60338 0.00000 0.00000 ; CB- CA- N- H1 6 1 2 24 3 0.65084 1.95253 0.00000 -2.60338 0.00000 0.00000 ; CB- CA- N- H2 6 1 2 25 3 0.65084 1.95253 0.00000 -2.60338 0.00000 0.00000 ; CB- CA- N- H3 6 1 3 4 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; CB- CA- C- O 6 1 3 5 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; CB- CA- C- OXT 6 7 8 9 3 3.68192 3.09616 -2.09200 -3.01248 0.00000 0.00000 ; CB- CG- CD- CE 6 7 8 16 3 0.66944 2.00832 0.00000 -2.67776 0.00000 0.00000 ; CB- CG- CD- HD2 6 7 8 17 3 0.66944 2.00832 0.00000 -2.67776 0.00000 0.00000 ; CB- CG- CD- HD3 7 8 9 10 3 0.65084 1.95253 0.00000 -2.60338 0.00000 0.00000 ; CG- CD- CE- NZ 7 8 9 18 3 0.65084 1.95253 0.00000 -2.60338 0.00000 0.00000 ; CG- CD- CE- HE2 7 8 9 19 3 0.65084 1.95253 0.00000 -2.60338 0.00000 0.00000 ; CG- CD- CE- HE3 8 7 6 12 3 0.66944 2.00832 0.00000 -2.67776 0.00000 0.00000 ; CD- CG- CB- HB2 8 7 6 13 3 0.66944 2.00832 0.00000 -2.67776 0.00000 0.00000 ; CD- CG- CB- HB3 8 9 10 20 3 0.65084 1.95253 0.00000 -2.60338 0.00000 0.00000 ; CD- CE- NZ- HZ1 8 9 10 21 3 0.65084 1.95253 0.00000 -2.60338 0.00000 0.00000 ; CD- CE- NZ- HZ2 8 9 10 22 3 0.65084 1.95253 0.00000 -2.60338 0.00000 0.00000 ; CD- CE- NZ- HZ3 9 8 7 14 3 0.66944 2.00832 0.00000 -2.67776 0.00000 0.00000 ; CE- CD- CG- HG2 9 8 7 15 3 0.66944 2.00832 0.00000 -2.67776 0.00000 0.00000 ; CE- CD- CG- HG3 10 9 8 16 3 0.65084 1.95253 0.00000 -2.60338 0.00000 0.00000 ; NZ- CE- CD- HD2 10 9 8 17 3 0.65084 1.95253 0.00000 -2.60338 0.00000 0.00000 ; NZ- CE- CD- HD3 11 1 2 23 3 0.65084 1.95253 0.00000 -2.60338 0.00000 0.00000 ; HA- CA- N- H1 11 1 2 24 3 0.65084 1.95253 0.00000 -2.60338 0.00000 0.00000 ; HA- CA- N- H2 11 1 2 25 3 0.65084 1.95253 0.00000 -2.60338 0.00000 0.00000 ; HA- CA- N- H3 11 1 3 4 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; HA- CA- C- O 11 1 3 5 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ; HA- CA- C- OXT 11 1 6 7 3 0.65084 1.95253 0.00000 -2.60338 0.00000 0.00000 ; HA- CA- CB- CG 11 1 6 12 3 0.65084 1.95253 0.00000 -2.60338 0.00000 0.00000 ; HA- CA- CB- HB2 11 1 6 13 3 0.65084 1.95253 0.00000 -2.60338 0.00000 0.00000 ; HA- CA- CB- HB3 12 6 7 14 3 0.62760 1.88280 0.00000 -2.51040 0.00000 0.00000 ; HB2- CB- CG- HG2 12 6 7 15 3 0.62760 1.88280 0.00000 -2.51040 0.00000 0.00000 ; HB2- CB- CG- HG3 13 6 7 14 3 0.62760 1.88280 0.00000 -2.51040 0.00000 0.00000 ; HB3- CB- CG- HG2 13 6 7 15 3 0.62760 1.88280 0.00000 -2.51040 0.00000 0.00000 ; HB3- CB- CG- HG3 14 7 8 16 3 0.62760 1.88280 0.00000 -2.51040 0.00000 0.00000 ; HG2- CG- CD- HD2 14 7 8 17 3 0.62760 1.88280 0.00000 -2.51040 0.00000 0.00000 ; HG2- CG- CD- HD3 15 7 8 16 3 0.62760 1.88280 0.00000 -2.51040 0.00000 0.00000 ; HG3- CG- CD- HD2 15 7 8 17 3 0.62760 1.88280 0.00000 -2.51040 0.00000 0.00000 ; HG3- CG- CD- HD3 16 8 9 18 3 0.65084 1.95253 0.00000 -2.60338 0.00000 0.00000 ; HD2- CD- CE- HE2 16 8 9 19 3 0.65084 1.95253 0.00000 -2.60338 0.00000 0.00000 ; HD2- CD- CE- HE3 17 8 9 18 3 0.65084 1.95253 0.00000 -2.60338 0.00000 0.00000 ; HD3- CD- CE- HE2 17 8 9 19 3 0.65084 1.95253 0.00000 -2.60338 0.00000 0.00000 ; HD3- CD- CE- HE3 18 9 10 20 3 0.65084 1.95253 0.00000 -2.60338 0.00000 0.00000 ; HE2- CE- NZ- HZ1 18 9 10 21 3 0.65084 1.95253 0.00000 -2.60338 0.00000 0.00000 ; HE2- CE- NZ- HZ2 18 9 10 22 3 0.65084 1.95253 0.00000 -2.60338 0.00000 0.00000 ; HE2- CE- NZ- HZ3 19 9 10 20 3 0.65084 1.95253 0.00000 -2.60338 0.00000 0.00000 ; HE3- CE- NZ- HZ1 19 9 10 21 3 0.65084 1.95253 0.00000 -2.60338 0.00000 0.00000 ; HE3- CE- NZ- HZ2 19 9 10 22 3 0.65084 1.95253 0.00000 -2.60338 0.00000 0.00000 ; HE3- CE- NZ- HZ3 [ dihedrals ] ; impropers ; treated as propers in GROMACS to use correct AMBER analytical function ; i j k l func phase kd pn 1 4 3 5 1 180.00 4.60240 2 ; CA- O- C- OXT [ system ] LIG [ molecules ] ; Compound nmols LIG 1