; POPC model using Gromos 53a6 forcefield ; atom numbering taken from POPC model with Berger et al forcefield (obtained from P. Tieleman) ; ; Please cite: ; Kukol, A (2009), Lipid Models for United-Atom Molecular Dynamics Simulations of Proteins, ; J Chem Theo Comput, available from http://pubs.acs.org/journal/jctcce, DOI: 10.1021/ct8003468 ; ---------------------------- ; the dihedral phi2 (include multiplicity zero) was expressed as Ryckaert-Belleman function ; for compatibility with Gromacs 4.x ; AK (2/6/2009) [ moleculetype ] ; Name nrexcl POPC 3 [ atoms ] ; nr type resnr residu atom cgnr charge mass 1 CH3 1 POPC C1 0 0.4 15.0350 ; qtot:0.36 2 CH3 1 POPC C2 0 0.4 15.0350 ; qtot:0.72 3 CH3 1 POPC C3 0 0.4 15.0350 ; qtot:1.08 4 NL 1 POPC N4 0 -0.5 14.0067 ; qtot:0.76 5 CH2 1 POPC C5 0 0.3 14.0270 ; qtot:1.0 6 CH2 1 POPC C6 1 0.4 14.0270 ; qtot:1.0 7 OA 1 POPC O7 1 -0.8 15.9994 ; qtot:0.54 8 P 1 POPC P8 1 1.7 30.9738 ; qtot:2.3 9 OM 1 POPC O9 1 -0.8 15.9994 ; qtot:1.5 10 OM 1 POPC O10 1 -0.8 15.9994 ; qtot:0.7 11 OA 1 POPC O11 1 -0.7 15.9994 ; qtot:0 12 CH2 1 POPC C12 2 0.4 14.0270 ; qtot:0.08 13 CH1 1 POPC C13 2 0.3 13.0190 ; qtot:0.52 14 OE 1 POPC O14 2 -0.7 15.9994 ; qtot:-0.14 15 CH0 1 POPC C15 2 0.7 12.0110 ; qtot:0.56 16 O 1 POPC O16 2 -0.7 15.9994 ; qtot:0.0 17 CH2 1 POPC C17 3 0 14.0270 ; qtot: 18 CH2 1 POPC C18 4 0 14.0270 ; qtot: 19 CH2 1 POPC C19 5 0 14.0270 ; qtot: 20 CH2 1 POPC C20 6 0 14.0270 ; qtot: 21 CH2 1 POPC C21 7 0 14.0270 ; qtot: 22 CH2 1 POPC C22 8 0 14.0270 ; qtot: 23 CH2 1 POPC C23 9 0 14.0270 ; qtot: 24 CR1 1 POPC C24 10 0 13.0190 ; qtot: 25 CR1 1 POPC C25 11 0 13.0190 ; qtot: 26 CH2 1 POPC C26 12 0 14.0270 ; qtot: 27 CH2 1 POPC C27 13 0 14.0270 ; qtot: 28 CH2 1 POPC C28 14 0 14.0270 ; qtot: 29 CH2 1 POPC C29 15 0 14.0270 ; qtot: 30 CH2 1 POPC C30 16 0 14.0270 ; qtot: 31 CH2 1 POPC C31 17 0 14.0270 ; qtot: 32 CH2 1 POPC C32 18 0.5 14.0270 ; qtot: 33 OE 1 POPC O33 18 -0.7 15.9994 ; qtot: 34 CH0 1 POPC C34 18 0.8 12.0110 ; qtot: 35 O 1 POPC O35 18 -0.6 15.9994 ; qtot: 36 CH2 1 POPC C36 19 0 14.0270 ; qtot: 37 CH2 1 POPC C37 20 0 14.0270 ; qtot: 38 CH2 1 POPC C38 21 0 14.0270 ; qtot: 39 CH2 1 POPC C39 22 0 14.0270 ; qtot: 40 CH2 1 POPC C40 23 0 14.0270 ; qtot: 41 CH2 1 POPC C41 24 0 14.0270 ; qtot: 42 CH2 1 POPC C42 25 0 14.0270 ; qtot: 43 CH2 1 POPC C43 26 0 14.0270 ; qtot: 44 CH2 1 POPC C44 27 0 14.0270 ; qtot: 45 CH2 1 POPC C45 28 0 14.0270 ; qtot: 46 CH2 1 POPC C46 29 0 14.0270 ; qtot: 47 CH2 1 POPC C47 30 0 14.0270 ; qtot: 48 CH2 1 POPC C48 31 0 14.0270 ; qtot: 49 CH2 1 POPC C49 32 0 14.0270 ; qtot: 50 CH3 1 POPC C50 33 0 15.0350 ; qtot: 51 CH2 1 POPC CA1 34 0 14.0270 ; tail2 52 CH3 1 POPC CA2 35 0 15.0350; tail2 [ bonds ] ; ai aj funct 4 5 2 gb_21 5 6 2 gb_27 6 7 2 gb_18 7 8 2 gb_28 8 9 2 gb_24 8 10 2 gb_24 8 11 2 gb_28 11 12 2 gb_18 12 13 2 gb_27 13 14 2 gb_18 13 32 2 gb_27 14 15 2 gb_10 15 16 2 gb_5 15 17 2 gb_23 17 18 2 gb_27 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_10 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 30 31 2 gb_27 31 51 2 gb_27 51 52 2 gb_27 32 33 2 gb_18 33 34 2 gb_10 34 35 2 gb_5 34 36 2 gb_23 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 47 48 2 gb_27 48 49 2 gb_27 49 50 2 gb_27 1 4 2 gb_21 2 4 2 gb_21 3 4 2 gb_21 [ pairs ] ; ai aj funct not modified yet (AK, 25/04/08) 1 6 1 2 6 1 3 6 1 4 7 1 5 8 1 6 9 1 6 10 1 6 11 1 7 12 1 8 13 1 9 12 1 10 12 1 11 14 1 11 32 1 12 15 1 12 33 1 13 16 1 13 17 1 13 34 1 14 18 1 14 33 1 15 19 1 15 32 1 16 18 1 22 25 1 ; pair around double bond 24 27 1 ; pair around double bond 32 35 1 32 36 1 33 37 1 34 38 1 35 37 1 [ angles ] ; ai aj ak funct 4 5 6 2 ga_15 5 6 7 2 ga_15 6 7 8 2 ga_26 7 8 9 2 ga_14 7 8 10 2 ga_14 7 8 11 2 ga_5 8 11 12 2 ga_26 9 8 10 2 ga_29 9 8 11 2 ga_14 10 8 11 2 ga_14 11 12 13 2 ga_15 12 13 14 2 ga_13 12 13 32 2 ga_13 13 14 15 2 ga_22 13 32 33 2 ga_15 14 13 32 2 ga_13 14 15 16 2 ga_31 14 15 17 2 ga_16 15 17 18 2 ga_15 16 15 17 2 ga_35 17 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_27; double bond 24 25 26 2 ga_27; double bond 25 26 27 2 ga_15 26 27 28 2 ga_15 27 28 29 2 ga_15 28 29 30 2 ga_15 29 30 31 2 ga_15 30 31 51 2 ga_15 31 51 52 2 ga_15 32 33 34 2 ga_22 33 34 35 2 ga_31 33 34 36 2 ga_16 34 36 37 2 ga_15 35 34 36 2 ga_35 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 46 47 48 2 ga_15 47 48 49 2 ga_15 48 49 50 2 ga_15 1 4 2 2 ga_13 2 4 3 2 ga_13 3 4 1 2 ga_13 1 4 5 2 ga_13 2 4 5 2 ga_13 3 4 5 2 ga_13 [ dihedrals ] ; ai aj ak al funct phi0 cp mult 1 4 5 6 1 gd_29 4 5 6 7 1 gd_4 4 5 6 7 1 gd_36 5 6 7 8 1 gd_29 6 7 8 11 1 gd_20 6 7 8 11 1 gd_27 7 8 11 12 1 gd_20 7 8 11 12 1 gd_27 8 11 12 13 1 gd_29 11 12 13 14 1 gd_34 11 12 13 32 1 gd_34 11 12 13 32 1 gd_17 ; this dihedral is not in DPPC 12 13 32 33 1 gd_34 12 13 32 33 1 gd_17 ; this dihedral is not in DPPC 12 13 14 15 1 gd_29 13 32 33 34 1 gd_29 13 14 15 17 1 gd_13 14 13 32 33 1 gd_18 14 15 17 18 1 gd_40 15 17 18 19 1 gd_34 17 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 0 3.350 1 ;phi3 (from Martinez-Seara et al. 2008) 21 22 23 24 1 180 1.660 2 21 22 23 24 1 0 7.333 3 22 23 24 25 3 2.885 4.17 7.8 4.4 0.0 0.0 ;phi2 (Ryckhaert-Belleman function) 24 25 26 27 3 2.885 4.17 7.8 4.4 0.0 0.0 ;phi2' (Ryckhaert-Belleman function) 25 26 27 28 1 0 3.350 1 ;phi3' 25 26 27 28 1 180 1.660 2 25 26 27 28 1 0 7.333 3 26 27 28 29 1 gd_34 27 28 29 30 1 gd_34 28 29 30 31 1 gd_34 29 30 31 51 1 gd_34 30 31 51 52 1 gd_34 13 32 33 34 1 gd_29 32 33 34 36 1 gd_13 33 34 36 37 1 gd_40 34 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 45 46 47 48 1 gd_34 46 47 48 49 1 gd_34 47 48 49 50 1 gd_34 [ dihedrals ] ; ai aj ak al funct 13 14 32 12 2 gi_2 15 14 17 16 2 gi_1 34 33 36 35 2 gi_1 23 24 25 26 2 gi_1 ; double bond #ifdef POSRES_LIPID #include "lipid_posre.itp" #endif