[ defaults ] ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ 1 3 no 1.0 0.0 [ atomtypes ] ; name mass charge ptype sigma epsilon n 14.00670 0.000 A 0.32500 0.71128 c1 12.01100 0.000 A 0.35500 0.29288 c2 12.01100 0.000 A 0.35500 0.29288 c3 12.01100 0.000 A 0.35500 0.29288 h1 1.00790 0.000 A 0.24200 0.12552 h2 1.00790 0.000 A 0.24200 0.12552 h3 1.00790 0.000 A 0.24200 0.12552 [ moleculetype ] ; Name nrexcl piri 6 [ atoms ] ; nr type resnr residue atom cgnr charge mass 1 n 1 piri n 11 -0.6780 14.0067 2 c1 1 piri c1 1 0.4730 12.0110 3 c2 1 piri c2 3 -0.4470 12.0110 4 c3 1 piri c3 5 0.2270 12.0110 5 c2 1 piri c2 7 -0.4470 12.0110 6 c1 1 piri c1 9 0.4730 12.0110 7 h1 1 piri h1 2 0.0120 1.0079 8 h2 1 piri h2 4 0.1550 1.0079 9 h3 1 piri h3 6 0.0650 1.0079 10 h2 1 piri h2 8 0.1550 1.0079 11 h1 1 piri h1 10 0.0120 1.0079 ; Stretchings [ bonds ] 1 2 1 0.1340 278911.407 ; 1 n=c1 2 3 1 0.1399 308534.663 ; 2 c1=c2 3 4 1 0.1396 340293.661 ; 3 c2=c3 4 5 1 0.1397 340293.661 ; 4 c3=c2 1 6 1 0.1341 278911.407 ; 5 n=c1 5 6 1 0.1398 308534.663 ; 6 c2=c1 2 7 1 0.1096 324316.834 ; 7 c1-h1 3 8 1 0.1092 334879.636 ; 8 c2-h2 4 9 1 0.1093 331744.076 ; 9 c3-h3 5 10 1 0.1092 334879.636 ; 10 c2-h2 6 11 1 0.1096 324316.834 ; 11 c1-h1 ; Bendings [ angles ] 1 2 3 1 123.90 994.3146 ; 12 n=c1=c2 2 1 6 1 116.90 600.6121 ; 13 c1=n=c1 1 2 7 1 115.95 432.2184 ; 14 n=c1-h1 2 3 4 1 118.42 667.8750 ; 15 c1=c2=c3 3 2 7 1 120.15 280.8957 ; 16 h1-c1=c2 2 3 8 1 120.29 342.6350 ; 17 c1=c2-h2 3 4 5 1 118.44 629.9741 ; 18 c2=c3=c2 4 3 8 1 121.29 312.8768 ; 19 h2-c2=c3 3 4 9 1 120.79 318.9085 ; 20 c2=c3-h3 4 5 6 1 118.44 667.8750 ; 21 c3=c2=c1 5 4 9 1 120.77 318.9085 ; 22 h3-c3=c2 4 5 10 1 121.25 312.8768 ; 23 c3=c2-h2 1 6 5 1 123.89 994.3146 ; 24 n=c1=c2 1 6 11 1 115.93 432.2184 ; 25 n=c1-h1 6 5 10 1 120.31 342.6350 ; 26 h2-c2=c1 5 6 11 1 120.18 280.8957 ; 27 c2=c1-h1 ; Torsions [ dihedrals ] ; stiff dieds 1 2 3 4 2 -0.0 61.227 ; 28 n=c1=c2=c3 6 1 2 3 2 0.0 74.860 ; 29 c1=n=c1=c2 1 2 3 8 2 180.0 59.794 ; 30 n=c1=c2-h2 2 1 6 5 2 0.0 74.860 ; 31 c2=c1=n=c1 6 1 2 7 2 180.0 89.112 ; 32 c1=n=c1-h1 2 1 6 11 2 180.0 89.112 ; 33 h1-c1=n=c1 2 3 4 5 2 -0.0 66.562 ; 34 c1=c2=c3=c2 7 2 3 4 2 180.0 56.931 ; 35 h1-c1=c2=c3 2 3 4 9 2 -180.0 59.768 ; 36 c1=c2=c3-h3 7 2 3 8 2 0.0 23.120 ; 37 h1-c1=c2-h2 3 4 5 6 2 0.1 66.562 ; 38 c2=c3=c2=c1 8 3 4 5 2 180.0 76.071 ; 39 h2-c2=c3=c2 3 4 5 10 2 -180.0 76.071 ; 40 c2=c3=c2-h2 8 3 4 9 2 -0.0 32.038 ; 41 h2-c2=c3-h3 4 5 6 1 2 -0.1 61.227 ; 42 c3=c2=c1=n 9 4 5 6 2 -180.0 59.768 ; 43 h3-c3=c2=c1 4 5 6 11 2 -180.0 56.931 ; 44 c3=c2=c1-h1 9 4 5 10 2 0.0 32.038 ; 45 h3-c3=c2-h2 10 5 6 1 2 180.0 59.794 ; 46 n=c1=c2-h2 10 5 6 11 2 0.0 23.120 ; 47 h2-c2=c1-h1 ; star-like dieds 7 1 3 2 2 0.0 217.356 ; 48 c1=c2--n--h1 * 8 2 4 3 2 -0.0 89.309 ; 49 c2=c3--c1--h2 * 9 3 5 4 2 -0.0 151.273 ; 50 c3=c2--c2--h3 * 10 4 6 5 2 0.0 89.288 ; 51 c2=c1--c3--h2 * 11 1 5 6 2 0.0 217.356 ; 52 c1=c2--n--h1 * ; Exclusions from default nonbonded [ exclusions ] ; ai aj 1 2 1 3 1 4 1 5 1 6 1 7 1 8 1 9 1 10 1 11 2 3 2 4 2 5 2 6 2 7 2 8 2 9 2 10 2 11 3 4 3 5 3 6 3 7 3 8 3 9 3 10 3 11 4 5 4 6 4 7 4 8 4 9 4 10 4 11 5 6 5 7 5 8 5 9 5 10 5 11 6 7 6 8 6 9 6 10 6 11 7 8 7 9 7 10 7 11 8 9 8 10 8 11 9 10 9 11 10 11 [ system ] ; Name Pyridine [ molecules ] ; Compound ;mols piri 1