;;; MARTINI 2.1 coarse-grained topology ;;;;; Martini lipid topology for Porphyromonas gingivalis Lipid A (Lipopolysaccharide) ;;;;;;;;;;; ; ; Reference(s): ; Ma, Huilin, Daniel D. Cummins, Natalie Brooke Edelstein, Jerry Gomez, Aliza Khan, Masud Dikita Llewellyn, Tara Picudella, ; Sarah Rose Willsey, and Shikha Nangia. "Modeling diversity in structures of bacterial outer membrane lipids." ; Journal of chemical theory and computation 13, 811-824 (2017). ; ; Created by Huilin Ma and Shikha Nangia 2017.01.12 ; ;----------------Bead Map------------------- ; Phosphate(5) ; XYA (1-5)---4---6----SYB (6-9) ; 2 3 9 8 ; A B C D ; | | | | ; 10 14 19 28 ; | | | | | ; | 15 20 24 29 ; 11 16 21 25 30 ; 12 17 22 26 31 ; 13 18 23 27 ;------------------------------------------ [moleculetype] ;molname exclusions PGIN 1 [atoms] ; id type resnr residu atom cgnr charge 1 P2 1 XYA L1 1 0.000 ; 2 P4 1 XYA L2 2 0.000 ; 3 P4 1 XYA L3 3 0.000 ; 4 P1 1 XYA L4 4 0.000 ; 5 Qa 1 XYA POX1 5 -1.000 ; 6 P2 1 SYB L6 6 0.000 ; 7 P1 1 SYB L7 7 0.000 ; 8 P1 1 SYB L8 8 0.000 ; 9 P5 1 SYB L9 9 0.000 ; 10 Na 1 LA1 LANA 10 0.000 ; 11 C1 1 LPA C1A1 11 0.000 ; 12 C1 1 LPA C2A1 12 0.000 ; 13 C1 1 LPA C3A1 13 0.000 ; 14 Na 1 LB1 LBNA 14 0.000 ; 15 C1 1 LPB C1B1 15 0.000 ; 16 C1 1 LPB C2B1 16 0.000 ; 17 C1 1 LPB C3B1 17 0.000 ; 18 C1 1 LPB C4B1 18 0.000 ; 19 Na 1 LC1 LCNA 19 0.000 ; 20 C1 1 LPC C1C1 20 0.000 ; 21 C1 1 LPC C2C1 21 0.000 ; 22 C1 1 LPC C3C1 22 0.000 ; 23 C1 1 LPC C4C1 23 0.000 ; 24 C1 1 LPC C1C2 24 0.000 ; 25 C1 1 LPC C2C2 25 0.000 ; 26 C1 1 LPC C3C2 26 0.000 ; 27 C1 1 LPC C4C2 27 0.000 ; 28 Na 1 LD1 LDNA 28 0.000 ; 29 C1 1 LPD C1D1 29 0.000 ; 30 C1 1 LPD C2D1 30 0.000 ; 31 C1 1 LPD C3D1 31 0.000 ; [ bonds ] ; i j funct length force.c. 4 6 1 0.470 5000 ; 4 1 1 0.320 5000 ; 4 3 1 0.320 5000 ; 1 3 1 0.320 5000 ; 1 5 1 0.320 5000 ; 1 2 1 0.320 1250 ; 7 8 1 0.470 5000 ; 7 6 1 0.300 5000 ; 6 8 1 0.300 5000 ; 6 9 1 0.470 5000 ; 2 10 1 0.470 1250 ; 10 11 1 0.470 1250 ; 11 12 1 0.470 1250 ; 12 13 1 0.470 1250 ; 3 14 1 0.470 1250 ; 14 15 1 0.470 1250 ; 15 16 1 0.470 1250 ; 16 17 1 0.470 1250 ; 17 18 1 0.470 1250 ; 9 19 1 0.470 1250 ; 19 20 1 0.470 5000 ; 20 21 1 0.470 1250 ; 21 22 1 0.470 1250 ; 22 23 1 0.470 1250 ; 19 24 1 0.470 1250 ; 24 25 1 0.470 1250 ; 25 26 1 0.470 1250 ; 26 27 1 0.470 1250 ; 8 28 1 0.470 1250 ; 28 29 1 0.470 1250 ; 29 30 1 0.470 1250 ; 30 31 1 0.470 1250 ; [angles] ; i j k funct angle force.c. 4 3 1 2 120.00 50. 3 1 5 2 120.00 50. 6 4 3 2 107.00 50. 7 6 8 2 59.00 50. 7 8 6 2 68.00 50. 2 10 11 2 180.00 25. 10 11 12 2 180.00 25. 11 12 13 2 180.00 25. 3 14 15 2 180.00 25. 14 15 16 2 180.00 25. 15 16 17 2 180.00 25. 16 17 18 2 180.00 25. 6 9 19 2 180.00 25. 20 19 24 2 120.00 50. 20 21 22 2 180.00 25. 21 22 23 2 180.00 25. 19 24 25 2 180.00 25. 24 25 26 2 180.00 25. 25 26 27 2 180.00 25. 6 8 28 2 101.00 50. 28 29 30 2 180.00 25. 29 30 31 2 180.00 25.