; POPG topology based on topology from Zhao et al., Biophys. J. 2007 ; D-POPG and L-POPG are built up separately according to their chiralities with C4(see the molecular ; structure for labeling) ; ; 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 LPOPG 3 [ atoms ] ; nr type resnr residu atom cgnr charge mass 1 H 1 LPOPG H1 0 0.4170 1.0080 ; qtot:0.36 2 OA 1 LPOPG O2 0 -0.5740 15.9994 ; qtot:0.72 3 CH2 1 LPOPG C3 0 0.1570 14.0270 ; qtot:1.08 4 CH1 1 LPOPG C4 1 0.1570 13.0190 ; qtot:0.76 5 OA 1 LPOPG O5 1 -0.5740 15.9994 ; qtot:1.0 6 H 1 LPOPG H6 1 0.4170 1.0080 ; qtot:1.0 7 CH2 1 LPOPG C7 2 0.4000 14.0270 ; 8 OE 1 LPOPG O8 2 -0.800 15.9994 ; qtot:0.54 9 P 1 LPOPG P9 2 1.700 30.9738 ; qtot:2.3 10 OM 1 LPOPG O10 2 -0.800 15.9994 ; qtot:1.5 11 OM 1 LPOPG O11 2 -0.800 15.9994 ; qtot:0.7 12 OE 1 LPOPG O12 2 -0.700 15.9994 ; qtot:0 13 CH2 1 LPOPG C13 3 0.400 14.0270 ; qtot:0.08 14 CH1 1 LPOPG C14 3 0.300 13.0190 ; qtot:0.52 15 OE 1 LPOPG O15 3 -0.700 15.9994 ; qtot:-0.14 16 CH0 1 LPOPG C16 3 0.7000 12.0110 ; qtot:0.56 17 O 1 LPOPG O17 3 -0.700 15.9994 ; qtot:0.0 18 CH2 1 LPOPG C18 4 0.0 14.0270 ; qtot: 19 CH2 1 LPOPG C19 5 0 14.0270 ; qtot: 20 CH2 1 LPOPG C20 6 0 14.0270 ; qtot: 21 CH2 1 LPOPG C21 7 0 14.0270 ; qtot: 22 CH2 1 LPOPG C22 8 0 14.0270 ; qtot: 23 CH2 1 LPOPG C23 9 0 14.0270 ; qtot: 24 CH2 1 LPOPG C24 10 0 14.0270 ; qtot: 25 CR1 1 LPOPG C25 11 0 13.0190 ; qtot: 26 CR1 1 LPOPG C26 12 0 13.0190 ; qtot: 27 CH2 1 LPOPG C27 13 0 14.0270 ; qtot: 28 CH2 1 LPOPG C28 14 0 14.0270 ; qtot: 29 CH2 1 LPOPG C29 15 0 14.0270 ; qtot: 30 CH2 1 LPOPG C30 16 0 14.0270 ; qtot: 31 CH2 1 LPOPG C31 17 0 14.0270 ; qtot: 32 CH2 1 LPOPG C32 18 0 14.0270 ; qtot: 33 CH2 1 LPOPG C33 19 0 14.0270 ; qtot: 34 CH3 1 LPOPG C34 20 0 15.0350 ; 35 CH2 1 LPOPG C35 21 0.50 14.0270 ; qtot: 36 OE 1 LPOPG O36 21 -0.70 15.9994 ; qtot: 37 CH0 1 LPOPG C37 21 0.80 12.0110 ; qtot: 38 O 1 LPOPG O38 21 -0.60 15.9994 ; qtot: 39 CH2 1 LPOPG C39 22 0 14.0270 ; qtot: 40 CH2 1 LPOPG C40 23 0 14.0270 ; qtot: 41 CH2 1 LPOPG C41 24 0 14.0270 ; qtot: 42 CH2 1 LPOPG C42 25 0 14.0270 ; qtot: 43 CH2 1 LPOPG C43 26 0 14.0270 ; qtot: 44 CH2 1 LPOPG C44 27 0 14.0270 ; qtot: 45 CH2 1 LPOPG C45 28 0 14.0270 ; qtot: 46 CH2 1 LPOPG C46 29 0 14.0270 ; qtot: 47 CH2 1 LPOPG C47 30 0 14.0270 ; qtot: 48 CH2 1 LPOPG C48 31 0 14.0270 ; qtot: 49 CH2 1 LPOPG C49 32 0 14.0270 ; qtot: 50 CH2 1 LPOPG C50 33 0 14.0270 ; qtot: 51 CH2 1 LPOPG C51 34 0 14.0270 ; qtot: 52 CH2 1 LPOPG C52 35 0 14.0270 ; qtot: 53 CH3 1 LPOPG C53 36 0 15.0350 ; qtot: [ bonds ] ; ai aj funct 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 35 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_10 ; double bond 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 32 2 gb_27 32 33 2 gb_27 33 34 2 gb_27 35 36 2 gb_18 36 37 2 gb_10 37 38 2 gb_5 37 39 2 gb_23 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 50 51 2 gb_27 51 52 2 gb_27 52 53 2 gb_27 1 2 2 gb_1 2 3 2 gb_13 3 4 2 gb_27 4 5 2 gb_13 5 6 2 gb_1 4 7 2 gb_27 [ pairs ] ; ai aj funct 2 5 1 ; leave as standard (A.K. 29/4/08) 2 7 1 3 8 1 5 8 1 4 9 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 35 1 13 16 1 13 36 1 14 17 1 14 18 1 14 37 1 15 19 1 15 36 1 16 20 1 16 35 1 17 19 1 23 26 1 ; pair around double bond 25 28 1 ; pair around double bond 35 38 1 35 39 1 36 40 1 37 41 1 38 40 1 [ angles ] ; ai aj ak funct 4 7 8 2 ga_15 7 8 9 2 ga_26 8 9 10 2 ga_14 8 9 11 2 ga_14 8 9 12 2 ga_5 9 12 13 2 ga_26 10 9 11 2 ga_29 10 9 12 2 ga_14 11 9 12 2 ga_14 12 13 14 2 ga_15 13 14 15 2 ga_13 13 14 35 2 ga_13 14 15 16 2 ga_22 14 35 36 2 ga_15 15 14 35 2 ga_13 15 16 17 2 ga_31 15 16 18 2 ga_16 16 18 19 2 ga_15 17 16 18 2 ga_35 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_27 ; double bond 25 26 27 2 ga_27 ; double bond 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 32 2 ga_15 31 32 33 2 ga_15 32 33 34 2 ga_15 35 36 37 2 ga_22 36 37 38 2 ga_31 36 37 39 2 ga_16 37 39 40 2 ga_15 38 37 39 2 ga_35 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 49 50 51 2 ga_15 50 51 52 2 ga_15 51 52 53 2 ga_15 1 2 3 2 ga_12 2 3 4 2 ga_13 3 4 5 2 ga_13 4 5 6 2 ga_12 5 4 7 2 ga_13 3 4 7 2 ga_13 4 7 8 2 ga_13 [ dihedrals ] ; ai aj ak al funct phi0 cp mult 1 2 3 4 1 gd_23 6 5 4 7 1 gd_23 5 4 7 8 1 gd_18 2 3 4 5 1 gd_18 2 3 4 7 1 gd_33 2 3 4 7 1 gd_17 3 4 5 6 1 gd_23 3 4 7 8 1 gd_33 3 4 7 8 1 gd_17 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 15 1 gd_34 12 13 14 35 1 gd_34 12 13 14 35 1 gd_17 13 14 35 36 1 gd_34 13 14 35 36 1 gd_17 13 14 15 16 1 gd_29 14 35 36 37 1 gd_29 14 15 16 18 1 gd_13 15 14 35 36 1 gd_18 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 0 3.350 1 ;this is phi3 22 23 24 25 1 180 1.660 2 22 23 24 25 1 0 7.333 3 23 24 25 26 3 2.885 4.17 7.8 4.4 0.0 0.0 ;phi2 (Ryckhaert-Belleman) 25 26 27 28 3 2.885 4.17 7.8 4.4 0.0 0.0 ;phi2' (Ryckhaert-Belleman) 26 27 28 29 1 0 3.350 1 ;this is phi3' 26 27 28 29 1 180 1.660 2 26 27 28 29 1 0 7.333 3 27 28 29 30 1 gd_34 28 29 30 31 1 gd_34 29 30 31 32 1 gd_34 30 31 32 33 1 gd_34 31 32 33 34 1 gd_34 14 35 36 37 1 gd_29 35 36 37 39 1 gd_13 36 37 39 40 1 gd_40 37 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 48 49 50 51 1 gd_34 49 50 51 52 1 gd_34 50 51 52 53 1 gd_34 [ dihedrals ] ; ai aj ak al funct 14 15 35 13 2 gi_2 16 15 18 17 2 gi_1 37 36 39 38 2 gi_1 24 25 26 27 2 gi_1 ; double bond C=C 4 5 7 3 2 -35.264 334.84617 ; L-stereochemistry at C4 #ifdef POSRES_LIPID #include "lipid_posre.itp" #endif