; ; GROMOS-CKP POPO. Thomas Piggot 2011 ; ; If you use this topology please read and cite: ; ; Electroporation of the E. coli and S. aureus Membranes: Molecular Dynamics Simulations of Complex Bacterial Membranes ; http://pubs.acs.org/doi/abs/10.1021/jp207013v ; [ moleculetype ] ; Name nrexcl POPO 3 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB 1 CH3 1 POPO C50' 1 0 15.035 ; 2 CH2 1 POPO C49' 2 0 14.027 ; 3 CH2 1 POPO C48' 2 0 14.027 ; 4 CH2 1 POPO C47' 3 0 14.027 ; 5 CH2 1 POPO C46' 3 0 14.027 ; 6 CH2 1 POPO C45' 4 0 14.027 ; 7 CH2 1 POPO C44' 4 0 14.027 ; 8 CH2 1 POPO C43' 5 0 14.027 ; 9 CH2 1 POPO C42' 5 0 14.027 ; 10 CH2 1 POPO C41' 6 0 14.027 ; 11 CH2 1 POPO C40' 6 0 14.027 ; 12 CH2 1 POPO C39' 7 0 14.027 ; 13 CH2 1 POPO C38' 7 0 14.027 ; 14 CH2 1 POPO C37' 8 0 14.027 ; 15 CH2 1 POPO C36' 8 0 14.027 ; 16 O 1 POPO O35' 9 -0.6 15.9994 ; 17 CH0 1 POPO C34' 9 0.8 12.011 ; 18 OE 1 POPO O33' 9 -0.7 15.9994 ; 19 CH2 1 POPO C32' 9 0.5 14.027 ; 20 CH3 1 POPO CA2' 10 0 15.035 ; 21 CH2 1 POPO CA1' 11 0 14.027 ; 22 CH2 1 POPO C31' 11 0 14.027 ; 23 CH2 1 POPO C30' 12 0 14.027 ; 24 CH2 1 POPO C29' 12 0 14.027 ; 25 CH2 1 POPO C28' 13 0 14.027 ; 26 CH2 1 POPO C27' 13 0 13.019 ; 27 CH2 1 POPO C26' 14 0 13.019 ; 28 CR1 1 POPO C25' 14 0 14.027 ; 29 CR1 1 POPO C24' 15 0 14.027 ; 30 CH2 1 POPO C23' 15 0 14.027 ; 31 CH2 1 POPO C22' 16 0 14.027 ; 32 CH2 1 POPO C21' 16 0 14.027 ; 33 CH2 1 POPO C20' 17 0 14.027 ; 34 CH2 1 POPO C19' 17 0 14.027 ; 35 CH2 1 POPO C18' 18 0 14.027 ; 36 CH2 1 POPO C17' 18 0 14.027 ; 37 O 1 POPO O16' 19 -0.7 15.9994 ; 38 CH0 1 POPO C15' 19 0.7 12.011 ; 39 OE 1 POPO O14' 19 -0.7 15.9994 ; 40 CH1 1 POPO C13' 19 0.3 13.019 ; 41 CH2 1 POPO C12' 19 0.4 14.027 ; 42 OA 1 POPO O11' 20 -0.7 15.9994 ; 43 OM 1 POPO O10' 20 -0.8 15.9994 ; 44 OM 1 POPO O9' 20 -0.8 15.9994 ; 45 P 1 POPO P8' 20 1.7 30.9738 ; 46 OA 1 POPO O7' 20 -0.8 15.9994 ; 47 CH2 1 POPO C6' 20 0.4 14.027 ; 48 CH1 1 POPO C3 21 0.157 13.019 ; 49 OA 1 POPO O4 21 -0.574 15.9994 ; 50 H 1 POPO H5 21 0.417 1.008 ; 51 CH2 1 POPO C6 22 0.4 14.027 ; 52 OA 1 POPO O7 22 -0.8 15.9994 ; 53 P 1 POPO P8 22 1.7 30.9738 ; 54 OM 1 POPO O9 22 -0.8 15.9994 ; 55 OM 1 POPO O10 22 -0.8 15.9994 ; 56 OA 1 POPO O11 22 -0.7 15.9994 ; 57 CH2 1 POPO C12 23 0.4 14.027 ; 58 CH1 1 POPO C13 23 0.3 13.019 ; 59 OE 1 POPO O14 23 -0.7 15.9994 ; 60 CH0 1 POPO C15 23 0.7 12.011 ; 61 O 1 POPO O16 23 -0.7 15.9994 ; 62 CH2 1 POPO C17 24 0 14.027 ; 63 CH2 1 POPO C18 24 0 14.027 ; 64 CH2 1 POPO C19 25 0 14.027 ; 65 CH2 1 POPO C20 25 0 14.027 ; 66 CH2 1 POPO C21 26 0 14.027 ; 67 CH2 1 POPO C22 26 0 14.027 ; 68 CH2 1 POPO C23 27 0 14.027 ; 69 CR1 1 POPO C24 27 0 14.027 ; 70 CR1 1 POPO C25 28 0 14.027 ; 71 CH2 1 POPO C26 28 0 13.019 ; 72 CH2 1 POPO C27 29 0 13.019 ; 73 CH2 1 POPO C28 29 0 14.027 ; 74 CH2 1 POPO C29 30 0 14.027 ; 75 CH2 1 POPO C30 30 0 14.027 ; 76 CH2 1 POPO C31 31 0 14.027 ; 77 CH2 1 POPO CA1 31 0 14.027 ; 78 CH3 1 POPO CA2 32 0 15.035 ; 79 CH2 1 POPO C32 33 0.5 14.027 ; 80 OE 1 POPO O33 33 -0.7 15.9994 ; 81 CH0 1 POPO C34 33 0.8 12.011 ; 82 O 1 POPO O35 33 -0.6 15.9994 ; 83 CH2 1 POPO C36 34 0 14.027 ; 84 CH2 1 POPO C37 34 0 14.027 ; 85 CH2 1 POPO C38 35 0 14.027 ; 86 CH2 1 POPO C39 35 0 14.027 ; 87 CH2 1 POPO C40 36 0 14.027 ; 88 CH2 1 POPO C41 36 0 14.027 ; 89 CH2 1 POPO C42 37 0 14.027 ; 90 CH2 1 POPO C43 37 0 14.027 ; 91 CH2 1 POPO C44 38 0 14.027 ; 92 CH2 1 POPO C45 38 0 14.027 ; 93 CH2 1 POPO C46 39 0 14.027 ; 94 CH2 1 POPO C47 39 0 14.027 ; 95 CH2 1 POPO C48 40 0 14.027 ; 96 CH2 1 POPO C49 40 0 14.027 ; 97 CH3 1 POPO C50 41 0 15.035 ; [ bonds ] ; ai aj funct c0 c1 c2 c3 1 2 2 gb_27 2 3 2 gb_27 3 4 2 gb_27 4 5 2 gb_27 5 6 2 gb_27 6 7 2 gb_27 7 8 2 gb_27 8 9 2 gb_27 9 10 2 gb_27 10 11 2 gb_27 11 12 2 gb_27 12 13 2 gb_27 13 14 2 gb_27 14 15 2 gb_27 15 17 2 gb_23 16 17 2 gb_5 17 18 2 gb_10 18 19 2 gb_18 19 40 2 gb_27 20 21 2 gb_27 21 22 2 gb_27 22 23 2 gb_27 23 24 2 gb_27 24 25 2 gb_27 25 26 2 gb_27 26 27 2 gb_27 27 28 2 gb_27 28 29 2 gb_10 29 30 2 gb_27 30 31 2 gb_27 31 32 2 gb_27 32 33 2 gb_27 33 34 2 gb_27 34 35 2 gb_27 35 36 2 gb_27 36 38 2 gb_23 37 38 2 gb_5 38 39 2 gb_10 39 40 2 gb_18 40 41 2 gb_27 41 42 2 gb_18 42 45 2 gb_28 43 45 2 gb_24 44 45 2 gb_24 45 46 2 gb_28 46 47 2 gb_18 47 48 2 gb_27 48 49 2 gb_18 48 51 2 gb_27 49 50 2 gb_1 51 52 2 gb_18 52 53 2 gb_28 53 54 2 gb_24 53 55 2 gb_24 53 56 2 gb_28 56 57 2 gb_18 57 58 2 gb_27 58 59 2 gb_18 58 79 2 gb_27 59 60 2 gb_10 60 61 2 gb_5 60 62 2 gb_23 62 63 2 gb_27 63 64 2 gb_27 64 65 2 gb_27 65 66 2 gb_27 66 67 2 gb_27 67 68 2 gb_27 68 69 2 gb_27 69 70 2 gb_10 70 71 2 gb_27 71 72 2 gb_27 72 73 2 gb_27 73 74 2 gb_27 74 75 2 gb_27 75 76 2 gb_27 76 77 2 gb_27 77 78 2 gb_27 79 80 2 gb_18 80 81 2 gb_10 81 82 2 gb_5 81 83 2 gb_23 83 84 2 gb_27 84 85 2 gb_27 85 86 2 gb_27 86 87 2 gb_27 87 88 2 gb_27 88 89 2 gb_27 89 90 2 gb_27 90 91 2 gb_27 91 92 2 gb_27 92 93 2 gb_27 93 94 2 gb_27 94 95 2 gb_27 95 96 2 gb_27 96 97 2 gb_27 [ pairs ] ; ai aj funct c0 c1 c2 c3 1 4 1 2 5 1 3 6 1 4 7 1 5 8 1 6 9 1 7 10 1 8 11 1 9 12 1 10 13 1 11 14 1 12 15 1 13 17 1 14 16 1 14 18 1 15 19 1 16 19 1 17 40 1 18 39 1 18 41 1 19 38 1 19 42 1 20 23 1 21 24 1 22 25 1 23 26 1 24 27 1 25 28 1 26 29 1 28 31 1 29 32 1 30 33 1 31 34 1 32 35 1 33 36 1 34 38 1 35 37 1 35 39 1 36 40 1 37 40 1 38 41 1 39 42 1 40 45 1 41 43 1 41 44 1 41 46 1 42 47 1 43 47 1 44 47 1 45 48 1 46 49 1 46 51 1 47 50 1 47 52 1 48 53 1 49 52 1 50 51 1 51 54 1 51 55 1 51 56 1 52 57 1 53 58 1 54 57 1 55 57 1 56 59 1 56 79 1 57 60 1 57 80 1 58 61 1 58 62 1 58 81 1 59 63 1 59 80 1 60 64 1 60 79 1 61 63 1 62 65 1 63 66 1 64 67 1 65 68 1 66 69 1 67 70 1 69 72 1 70 73 1 71 74 1 72 75 1 73 76 1 74 77 1 75 78 1 79 82 1 79 83 1 80 84 1 81 85 1 82 84 1 83 86 1 84 87 1 85 88 1 86 89 1 87 90 1 88 91 1 89 92 1 90 93 1 91 94 1 92 95 1 93 96 1 94 97 1 [ angles ] ; ai aj ak funct c0 c1 c2 c3 1 2 3 2 ga_15 2 3 4 2 ga_15 3 4 5 2 ga_15 4 5 6 2 ga_15 5 6 7 2 ga_15 6 7 8 2 ga_15 7 8 9 2 ga_15 8 9 10 2 ga_15 9 10 11 2 ga_15 10 11 12 2 ga_15 11 12 13 2 ga_15 12 13 14 2 ga_15 13 14 15 2 ga_15 14 15 17 2 ga_15 15 17 16 2 ga_35 15 17 18 2 ga_16 16 17 18 2 ga_31 17 18 19 2 ga_22 18 19 40 2 ga_15 20 21 22 2 ga_15 21 22 23 2 ga_15 22 23 24 2 ga_15 23 24 25 2 ga_15 24 25 26 2 ga_15 25 26 27 2 ga_15 26 27 28 2 ga_15 27 28 29 2 ga_27 28 29 30 2 ga_27 29 30 31 2 ga_15 30 31 32 2 ga_15 31 32 33 2 ga_15 32 33 34 2 ga_15 33 34 35 2 ga_15 34 35 36 2 ga_15 35 36 38 2 ga_15 36 38 37 2 ga_35 36 38 39 2 ga_16 37 38 39 2 ga_31 38 39 40 2 ga_22 19 40 39 2 ga_13 19 40 41 2 ga_13 39 40 41 2 ga_13 40 41 42 2 ga_15 41 42 45 2 ga_26 42 45 43 2 ga_14 42 45 44 2 ga_14 42 45 46 2 ga_5 43 45 44 2 ga_29 43 45 46 2 ga_14 44 45 46 2 ga_14 45 46 47 2 ga_26 46 47 48 2 ga_13 47 48 49 2 ga_13 47 48 51 2 ga_13 49 48 51 2 ga_13 48 49 50 2 ga_12 48 51 52 2 ga_13 51 52 53 2 ga_26 52 53 54 2 ga_14 52 53 55 2 ga_14 52 53 56 2 ga_5 54 53 55 2 ga_29 54 53 56 2 ga_14 55 53 56 2 ga_14 53 56 57 2 ga_26 56 57 58 2 ga_15 57 58 59 2 ga_13 57 58 79 2 ga_13 59 58 79 2 ga_13 58 59 60 2 ga_22 59 60 61 2 ga_31 59 60 62 2 ga_16 61 60 62 2 ga_35 60 62 63 2 ga_15 62 63 64 2 ga_15 63 64 65 2 ga_15 64 65 66 2 ga_15 65 66 67 2 ga_15 66 67 68 2 ga_15 67 68 69 2 ga_15 68 69 70 2 ga_27 69 70 71 2 ga_27 70 71 72 2 ga_15 71 72 73 2 ga_15 72 73 74 2 ga_15 73 74 75 2 ga_15 74 75 76 2 ga_15 75 76 77 2 ga_15 76 77 78 2 ga_15 58 79 80 2 ga_15 79 80 81 2 ga_22 80 81 82 2 ga_31 80 81 83 2 ga_16 82 81 83 2 ga_35 81 83 84 2 ga_15 83 84 85 2 ga_15 84 85 86 2 ga_15 85 86 87 2 ga_15 86 87 88 2 ga_15 87 88 89 2 ga_15 88 89 90 2 ga_15 89 90 91 2 ga_15 90 91 92 2 ga_15 91 92 93 2 ga_15 92 93 94 2 ga_15 93 94 95 2 ga_15 94 95 96 2 ga_15 95 96 97 2 ga_15 [ dihedrals ] ; ai aj ak al funct c0 c1 c2 c3 c4 c5 1 2 3 4 1 gd_34 2 3 4 5 1 gd_34 3 4 5 6 1 gd_34 4 5 6 7 1 gd_34 5 6 7 8 1 gd_34 6 7 8 9 1 gd_34 7 8 9 10 1 gd_34 8 9 10 11 1 gd_34 9 10 11 12 1 gd_34 10 11 12 13 1 gd_34 11 12 13 14 1 gd_34 12 13 14 15 1 gd_34 13 14 15 17 1 gd_34 14 15 17 18 1 gd_40 15 17 18 19 1 gd_13 17 18 19 40 1 gd_29 18 19 40 41 1 gd_34 20 21 22 23 1 gd_34 21 22 23 24 1 gd_34 22 23 24 25 1 gd_34 23 24 25 26 1 gd_34 24 25 26 27 1 gd_34 26 27 28 29 1 gd_34 27 28 29 30 1 gd_40 28 29 30 31 1 gd_40 29 30 31 32 1 gd_34 30 31 32 33 1 gd_34 31 32 33 34 1 gd_34 32 33 34 35 1 gd_34 33 34 35 36 1 gd_34 34 35 36 38 1 gd_34 35 36 38 39 1 gd_40 36 38 39 40 1 gd_13 38 39 40 41 1 gd_29 19 40 41 42 1 gd_34 40 41 42 45 1 gd_29 41 42 45 46 1 gd_27 41 42 45 46 1 gd_20 42 45 46 47 1 gd_27 42 45 46 47 1 gd_20 45 46 47 48 1 gd_29 46 47 48 51 1 gd_34 47 48 49 50 1 gd_23 47 48 51 52 1 gd_34 48 51 52 53 1 gd_29 51 52 53 56 1 gd_20 51 52 53 56 1 gd_27 52 53 56 57 1 gd_20 52 53 56 57 1 gd_27 53 56 57 58 1 gd_29 56 57 58 79 1 gd_34 57 58 59 60 1 gd_29 57 58 79 80 1 gd_34 58 59 60 62 1 gd_13 59 60 62 63 1 gd_40 60 62 63 64 1 gd_34 62 63 64 65 1 gd_34 63 64 65 66 1 gd_34 64 65 66 67 1 gd_34 65 66 67 68 1 gd_34 66 67 68 69 1 gd_34 67 68 69 70 1 gd_40 68 69 70 71 1 gd_40 69 70 71 72 1 gd_34 71 72 73 74 1 gd_34 72 73 74 75 1 gd_34 73 74 75 76 1 gd_34 74 75 76 77 1 gd_34 75 76 77 78 1 gd_34 58 79 80 81 1 gd_29 79 80 81 83 1 gd_13 80 81 83 84 1 gd_40 81 83 84 85 1 gd_34 83 84 85 86 1 gd_34 84 85 86 87 1 gd_34 85 86 87 88 1 gd_34 86 87 88 89 1 gd_34 87 88 89 90 1 gd_34 88 89 90 91 1 gd_34 89 90 91 92 1 gd_34 90 91 92 93 1 gd_34 91 92 93 94 1 gd_34 92 93 94 95 1 gd_34 93 94 95 96 1 gd_34 94 95 96 97 1 gd_34 [ dihedrals ] ; ai aj ak al funct c0 c1 c2 c3 16 15 18 17 2 gi_1 27 28 29 30 2 gi_1 37 36 39 38 2 gi_1 40 39 19 41 2 gi_2 ; R 57 79 59 58 2 gi_2 ; R 60 59 62 61 2 gi_1 68 69 70 71 2 gi_1 81 80 83 82 2 gi_1