; ; GROMOS-CKP L-DMPG. 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 LDMG 3 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB 1 H 1 LDMG H0 1 0.417 1.008 ; 2 OA 1 LDMG O1 1 -0.574 15.9994 ; 3 CH2 1 LDMG C2 1 0.157 14.027 ; 4 CH1 1 LDMG C3 2 0.157 13.019 ; 5 OA 1 LDMG O4 2 -0.574 15.9994 ; 6 H 1 LDMG H5 2 0.417 1.008 ; 7 CH2 1 LDMG C6 3 0.4 14.027 ; 8 OA 1 LDMG O7 3 -0.8 15.9994 ; 9 P 1 LDMG P8 3 1.7 30.9738 ; 10 OM 1 LDMG O9 3 -0.8 15.9994 ; 11 OM 1 LDMG O10 3 -0.8 15.9994 ; 12 OA 1 LDMG O11 3 -0.7 15.9994 ; 13 CH2 1 LDMG C12 4 0.4 14.027 ; 14 CH1 1 LDMG C13 4 0.3 13.019 ; 15 OE 1 LDMG O14 4 -0.7 15.9994 ; 16 CH0 1 LDMG C15 4 0.7 12.011 ; 17 O 1 LDMG O16 4 -0.7 15.9994 ; 18 CH2 1 LDMG C17 5 0 14.027 ; 19 CH2 1 LDMG C18 5 0 14.027 ; 20 CH2 1 LDMG C19 6 0 14.027 ; 21 CH2 1 LDMG C20 6 0 14.027 ; 22 CH2 1 LDMG C21 7 0 14.027 ; 23 CH2 1 LDMG C22 7 0 14.027 ; 24 CH2 1 LDMG C23 8 0 14.027 ; 25 CH2 1 LDMG C24 8 0 14.027 ; 26 CH2 1 LDMG C25 9 0 14.027 ; 27 CH2 1 LDMG C26 9 0 14.027 ; 28 CH2 1 LDMG C27 10 0 14.027 ; 29 CH2 1 LDMG C28 10 0 14.027 ; 30 CH3 1 LDMG C29 11 0 15.035 ; 31 CH2 1 LDMG C32 12 0.5 14.027 ; 32 OE 1 LDMG O33 12 -0.7 15.9994 ; 33 CH0 1 LDMG C34 12 0.8 12.011 ; 34 O 1 LDMG O35 12 -0.6 15.9994 ; 35 CH2 1 LDMG C36 13 0 14.027 ; 36 CH2 1 LDMG C37 13 0 14.027 ; 37 CH2 1 LDMG C38 14 0 14.027 ; 38 CH2 1 LDMG C39 14 0 14.027 ; 39 CH2 1 LDMG C40 15 0 14.027 ; 40 CH2 1 LDMG C41 15 0 14.027 ; 41 CH2 1 LDMG C42 16 0 14.027 ; 42 CH2 1 LDMG C43 16 0 14.027 ; 43 CH2 1 LDMG C44 17 0 14.027 ; 44 CH2 1 LDMG C45 17 0 14.027 ; 45 CH2 1 LDMG C46 18 0 14.027 ; 46 CH2 1 LDMG C47 18 0 14.027 ; 47 CH3 1 LDMG C48 19 0 15.035 ; [ bonds ] ; ai aj funct c0 c1 c2 c3 1 2 2 gb_1 2 3 2 gb_18 3 4 2 gb_27 4 5 2 gb_18 4 7 2 gb_27 5 6 2 gb_1 7 8 2 gb_18 8 9 2 gb_28 9 10 2 gb_24 9 11 2 gb_24 9 12 2 gb_28 12 13 2 gb_18 13 14 2 gb_27 14 15 2 gb_18 14 31 2 gb_27 15 16 2 gb_10 16 17 2 gb_5 16 18 2 gb_23 18 19 2 gb_27 19 20 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_27 29 30 2 gb_27 31 32 2 gb_18 32 33 2 gb_10 33 34 2 gb_5 33 35 2 gb_23 35 36 2 gb_27 36 37 2 gb_27 37 38 2 gb_27 38 39 2 gb_27 39 40 2 gb_27 40 41 2 gb_27 41 42 2 gb_27 42 43 2 gb_27 43 44 2 gb_27 44 45 2 gb_27 45 46 2 gb_27 46 47 2 gb_27 [ pairs ] ; ai aj funct c0 c1 c2 c3 1 4 1 2 5 1 2 7 1 3 6 1 3 8 1 4 9 1 5 8 1 6 7 1 7 10 1 7 11 1 7 12 1 8 13 1 9 14 1 10 13 1 11 13 1 12 15 1 12 31 1 13 16 1 13 32 1 14 17 1 14 18 1 14 33 1 15 19 1 15 32 1 16 20 1 16 31 1 17 19 1 18 21 1 19 22 1 20 23 1 21 24 1 22 25 1 23 26 1 24 27 1 25 28 1 26 29 1 27 30 1 31 34 1 31 35 1 32 36 1 33 37 1 34 36 1 35 38 1 36 39 1 37 40 1 38 41 1 39 42 1 40 43 1 41 44 1 42 45 1 43 46 1 44 47 1 [ angles ] ; ai aj ak funct c0 c1 c2 c3 1 2 3 2 ga_12 2 3 4 2 ga_13 3 4 5 2 ga_13 3 4 7 2 ga_13 5 4 7 2 ga_13 4 5 6 2 ga_12 4 7 8 2 ga_13 7 8 9 2 ga_26 8 9 10 2 ga_14 8 9 11 2 ga_14 8 9 12 2 ga_5 10 9 11 2 ga_29 10 9 12 2 ga_14 11 9 12 2 ga_14 9 12 13 2 ga_26 12 13 14 2 ga_15 13 14 15 2 ga_13 13 14 31 2 ga_13 15 14 31 2 ga_13 14 15 16 2 ga_22 15 16 17 2 ga_31 15 16 18 2 ga_16 17 16 18 2 ga_35 16 18 19 2 ga_15 18 19 20 2 ga_15 19 20 21 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_15 28 29 30 2 ga_15 14 31 32 2 ga_15 31 32 33 2 ga_22 32 33 34 2 ga_31 32 33 35 2 ga_16 34 33 35 2 ga_35 33 35 36 2 ga_15 35 36 37 2 ga_15 36 37 38 2 ga_15 37 38 39 2 ga_15 38 39 40 2 ga_15 39 40 41 2 ga_15 40 41 42 2 ga_15 41 42 43 2 ga_15 42 43 44 2 ga_15 43 44 45 2 ga_15 44 45 46 2 ga_15 45 46 47 2 ga_15 [ dihedrals ] ; ai aj ak al funct c0 c1 c2 c3 c4 c5 1 2 3 4 1 gd_23 2 3 4 7 1 gd_34 3 4 5 6 1 gd_23 3 4 7 8 1 gd_34 4 7 8 9 1 gd_29 7 8 9 12 1 gd_20 7 8 9 12 1 gd_27 8 9 12 13 1 gd_20 8 9 12 13 1 gd_27 9 12 13 14 1 gd_29 12 13 14 31 1 gd_34 13 14 15 16 1 gd_29 13 14 31 32 1 gd_34 14 15 16 18 1 gd_13 15 16 18 19 1 gd_40 16 18 19 20 1 gd_34 18 19 20 21 1 gd_34 19 20 21 22 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 25 26 27 28 1 gd_34 26 27 28 29 1 gd_34 27 28 29 30 1 gd_34 14 31 32 33 1 gd_29 31 32 33 35 1 gd_13 32 33 35 36 1 gd_40 33 35 36 37 1 gd_34 35 36 37 38 1 gd_34 36 37 38 39 1 gd_34 37 38 39 40 1 gd_34 38 39 40 41 1 gd_34 39 40 41 42 1 gd_34 40 41 42 43 1 gd_34 41 42 43 44 1 gd_34 42 43 44 45 1 gd_34 43 44 45 46 1 gd_34 44 45 46 47 1 gd_34 [ dihedrals ] ; ai aj ak al funct c0 c1 c2 c3 3 5 7 4 2 gi_2 ; L 13 31 15 14 2 gi_2 16 15 18 17 2 gi_1 33 32 35 34 2 gi_1