; GROMOS43A1-S3 sphingomyelin (SGML, SM) lipid ; extracted from Common PC lipids itp file 'lipids_43A1-S3.itp' ; ; Use ffG43A1-S3 parameter files ; KW-type potential (gd_kw20) is used for the dihedrals -CH2*-CH2*-CH2*-CH2*- ; of hydrocarbon chains. ; Partial charges on the head group atoms were derived from HF/6-31G* ; calculation ; Recommend to use VDW cutoff 1.6 nm and PME for electrostatic interaction with ; 1.0 nm cutoff in real space. ; ;References: ;[0]. S.-W. Chiu, S. A. Pandit, H. L. Scott, and E. Jakobsson. An ; improved united atom force field for simulation of mixed lipid ; bilayers. The Journal of Physical Chemistry B, 113 (9):2748-2763, ; 2009. 10.1021/jp807056c. URL ; http://pubs.acs.org/doi/abs/10.1021/jp807056c. ; ;[1]. Sagar A. Pandit, See-Wing Chiu, Eric Jakobsson, Ananth Grama, ; and H. L. Scott. Cholesterol Packing around Lipids with Saturated and ; Unsaturated Chains: A Simulation Study. Langmuir, 24: 6858-6865 ; (2008). ; ;[2]. Sagar A. Pandit, See-Wing Chiu, Eric Jakobsson, Ananth Grama, ; and H. L. Scott Cholesterol Surrogates: A Comparison of Cholesterol ; and 16:0 Ceramide in POPC Bilayers. Biophys. J. 2007 92: 920-927. ; ;[3]. Sagar A. Pandit, S. Vasudevan, S. W. Chiu, R. Jay Mashl, Eric ; Jakobsson, and H. L. Scott. Sphingomyelin-Cholesterol Domains in ; Phospholipid Membranes: Atomistic Simulation. Biophys. J. 2004 87: ; 1092-1100. ; ;[4]. S. W. Chiu, S. Vasudevan, Eric Jakobsson, R. Jay Mashl, and ; H. Larry Scott. Structure of Sphingomyelin Bilayers: A Simulation ; Study. Biophys. J. 2003 85: 3624-3636. ; [ moleculetype ] ; Name nrexcl SGML 3 ; SPHINGOMYELIN ; [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB 1 CH3* 1 SGML C1 1 0.40 15.035 ; qtot 0.4 2 CH3* 1 SGML C2 2 0.40 15.035 ; qtot 0.8 3 CH3* 1 SGML C3 3 0.40 15.035 ; qtot 1.2 4 NL 1 SGML N4 4 -0.5 14.0067 ; qtot 0.7 5 CH2* 1 SGML C5 5 0.3 14.027 ; qtot 1 6 CH2* 1 SGML C6 6 0.4 14.027 ; qtot 1.4 7 OA 1 SGML OS7 7 -0.8 15.9994 ; qtot 0.7 8 P 1 SGML P8 8 1.7 30.9738 ; qtot 2.3 9 OM* 1 SGML OM9 9 -0.8 15.9994 ; qtot 1.5 10 OM* 1 SGML OM10 10 -0.8 15.9994 ; qtot 0.7 11 OA 1 SGML OS11 11 -0.7 15.9994 ; qtot 0 12 CH2* 1 SGML C12 12 0.25 14.027 ; qtot 0.3 13 CH1* 1 SGML C13 13 0.15 13.019 ; qtot 0.5 14 N 1 SGML N14 14 -0.85 14.0067 ; qtot -0.3 15 H 1 SGML H15 15 0.45 1.008 ; qtot 0 16 CO* 1 SGML C16 16 0.70 12.011 ; qtot 0.8 17 O* 1 SGML O17 17 -0.70 15.9994 ; qtot 0.1 18 CH2* 1 SGML C18 18 0 14.027 ; qtot 0 19 CH2* 1 SGML C19 18 0 14.027 ; qtot 0 20 CH2* 1 SGML C20 18 0 14.027 ; qtot 0 21 CH2* 1 SGML C21 19 0 14.027 ; qtot 0 22 CH2* 1 SGML C22 19 0 14.027 ; qtot 0 23 CH2* 1 SGML C23 19 0 14.027 ; qtot 0 24 CH2* 1 SGML C24 20 0 14.027 ; qtot 0 25 CH2* 1 SGML C25 20 0 14.027 ; qtot 0 26 CH2* 1 SGML C26 20 0 14.027 ; qtot 0 27 CH2* 1 SGML C27 21 0 14.027 ; qtot 0 28 CH2* 1 SGML C28 21 0 14.027 ; qtot 0 29 CH2* 1 SGML C29 21 0 14.027 ; qtot 0 30 CH2* 1 SGML C30 22 0 14.027 ; qtot 0 31 CH2* 1 SGML C31 22 0 14.027 ; qtot 0 32 CH2* 1 SGML C32 22 0 14.027 ; qtot 0 33 CH2* 1 SGML C33 23 0 14.027 ; qtot 0 34 CH3* 1 SGML C34 23 0 15.035 ; qtot 0 35 CH1* 1 SGML C35 24 0.325 13.019 ; qtot 0.3 36 OA 1 SGML OA36 25 -0.760 15.9994 ; qtot -0.4 37 H 1 SGML H37 26 0.435 1.008 ; qtot 0 38 C*H1 1 SGML C38 27 0 13.019 ; qtot 0 39 C*H1 1 SGML C39 27 0 13.019 ; qtot 0 40 CH2* 1 SGML C40 27 0 14.027 ; qtot 0 41 CH2* 1 SGML C41 28 0 14.027 ; qtot 0 42 CH2* 1 SGML C42 28 0 14.027 ; qtot 0 43 CH2* 1 SGML C43 28 0 14.027 ; qtot 0 44 CH2* 1 SGML C44 29 0 14.027 ; qtot 0 45 CH2* 1 SGML C45 29 0 14.027 ; qtot 0 46 CH2* 1 SGML C46 29 0 14.027 ; qtot 0 47 CH2* 1 SGML C47 30 0 14.027 ; qtot 0 48 CH2* 1 SGML C48 30 0 14.027 ; qtot 0 49 CH2* 1 SGML C49 30 0 14.027 ; qtot 0 50 CH2* 1 SGML C50 31 0 14.027 ; qtot 0 51 CH2* 1 SGML C51 31 0 14.027 ; qtot 0 52 CH3* 1 SGML C52 31 0 15.035 ; qtot 0 [ bonds ] ; ai aj funct c0 c1 c2 c3 1 4 2 gb_20 2 4 2 gb_20 3 4 2 gb_20 4 5 2 gb_20 5 6 2 gb_26 6 7 2 gb_17 7 8 2 gb_27 8 9 2 gb_23 8 10 2 gb_23 8 11 2 gb_27 11 12 2 gb_17 12 13 2 gb_26 13 14 2 gb_20 13 35 2 gb_26 14 15 2 gb_2 14 16 2 gb_12 16 17 2 gb_4 16 18 2 gb_26a 18 19 2 gb_26 19 20 2 gb_26 20 21 2 gb_26 21 22 2 gb_26 22 23 2 gb_26 23 24 2 gb_26 24 25 2 gb_26 25 26 2 gb_26 26 27 2 gb_26 27 28 2 gb_26 28 29 2 gb_26 29 30 2 gb_26 30 31 2 gb_26 31 32 2 gb_26 32 33 2 gb_26 33 34 2 gb_26 35 36 2 gb_17 35 38 2 gb_58 36 37 2 gb_1 38 39 2 gb_57 39 40 2 gb_58 40 41 2 gb_26 41 42 2 gb_26 42 43 2 gb_26 43 44 2 gb_26 44 45 2 gb_26 45 46 2 gb_26 46 47 2 gb_26 47 48 2 gb_26 48 49 2 gb_26 49 50 2 gb_26 50 51 2 gb_26 51 52 2 gb_26 [ pairs ] ; ai aj funct c0 c1 c2 c3 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 35 1 12 36 1 14 36 1 14 38 1 15 35 1 16 35 1 35 40 1 36 39 1 [ angles ] ; ai aj ak funct c0 c1 c2 c3 1 4 2 2 ga_12 1 4 3 2 ga_12 1 4 5 2 ga_12 2 4 3 2 ga_12 2 4 5 2 ga_12 3 4 5 2 ga_12 4 5 6 2 ga_14 5 6 7 2 ga_14 6 7 8 2 ga_25 7 8 9 2 ga_13 7 8 10 2 ga_13 7 8 11 2 ga_4 9 8 10 2 ga_28 9 8 11 2 ga_13 10 8 11 2 ga_13 8 11 12 2 ga_25 11 12 13 2 ga_14 12 13 14 2 ga_12 12 13 35 2 ga_12 14 13 35 2 ga_12 13 14 15 2 ga_24 13 14 16 2 ga_30 15 14 16 2 ga_31a 14 16 17 2 ga_32a 14 16 18 2 ga_18 17 16 18 2 ga_34a 16 18 19 2 ga_14 18 19 20 2 ga_14 19 20 21 2 ga_14 20 21 22 2 ga_14 21 22 23 2 ga_14 22 23 24 2 ga_14 23 24 25 2 ga_14 24 25 26 2 ga_14 25 26 27 2 ga_14 26 27 28 2 ga_14 27 28 29 2 ga_14 28 29 30 2 ga_14 29 30 31 2 ga_14 30 31 32 2 ga_14 31 32 33 2 ga_14 32 33 34 2 ga_14 13 35 36 2 ga_14 13 35 38 2 ga_14 36 35 38 2 ga_12 35 36 37 2 ga_11 35 38 39 2 ga_47 38 39 40 2 ga_47 39 40 41 2 ga_49 40 41 42 2 ga_14 41 42 43 2 ga_14 42 43 44 2 ga_14 43 44 45 2 ga_14 44 45 46 2 ga_14 45 46 47 2 ga_14 46 47 48 2 ga_14 47 48 49 2 ga_14 48 49 50 2 ga_14 49 50 51 2 ga_14 50 51 52 2 ga_14 [ dihedrals ] ; ai aj ak al funct c0 c1 c2 c3 c4 c5 3 4 5 6 1 gd_17d ;gd_kw36 ; remove 1-4 pairs 1/2/3-6 4 5 6 7 3 gd_swc6n 5 6 7 8 1 gd_14 ; 6 7 8 11 1 gd_9 ; 6 7 8 11 1 gd_11 6 7 8 11 3 gd_s0911 ; = gd_9 + gd_11 ; 7 8 11 12 1 gd_9 ; 7 8 11 12 1 gd_11 7 8 11 12 3 gd_s0911 8 11 12 13 1 gd_14 11 12 13 35 1 gd_17c 12 13 35 38 3 gd_kw4a1 12 13 14 16 3 gd_kw12 13 14 16 18 3 gd_kw9 14 16 18 19 3 gd_kw10 16 18 19 20 3 gd_kw11 18 19 20 21 3 gd_kw20 19 20 21 22 3 gd_kw20 20 21 22 23 3 gd_kw20 21 22 23 24 3 gd_kw20 22 23 24 25 3 gd_kw20 23 24 25 26 3 gd_kw20 24 25 26 27 3 gd_kw20 25 26 27 28 3 gd_kw20 26 27 28 29 3 gd_kw20 27 28 29 30 3 gd_kw20 28 29 30 31 3 gd_kw20 29 30 31 32 3 gd_kw20 30 31 32 33 3 gd_kw20 31 32 33 34 3 gd_kw20 35 38 39 40 1 gd_5b 38 35 36 37 3 gd_kw33 13 35 38 39 3 gd_kw34b 38 39 40 41 3 gd_kw34b 39 40 41 42 3 gd_kw4a1 40 41 42 43 3 gd_kw20 41 42 43 44 3 gd_kw20 42 43 44 45 3 gd_kw20 43 44 45 46 3 gd_kw20 44 45 46 47 3 gd_kw20 45 46 47 48 3 gd_kw20 46 47 48 49 3 gd_kw20 47 48 49 50 3 gd_kw20 48 49 50 51 3 gd_kw20 49 50 51 52 3 gd_kw20 [ dihedrals ] ; ai aj ak al funct c0 c1 c2 c3 13 14 35 12 2 gi_2 14 16 13 15 2 gi_1 16 18 14 17 2 gi_1 35 36 38 13 2 gi_2