; GROMOS43A1-S3 cholesterol ; 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 CHOL 3 ;CHOLESTEROL [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB 1 CH2R6 1 CHOL C1 1 0.0 14.027 2 CH2R6 1 CHOL C2 2 0.0 14.027 3 CH1R6 1 CHOL C3 3 0.270 13.019 4 CH2R6 1 CHOL C4 4 0.0 14.027 5 C* 1 CHOL C5 5 0.0 12.011 6 C*HR6 1 CHOL C6 6 0.0 13.019 7 CH2R6 1 CHOL C7 7 0.0 14.027 8 CH1R6 1 CHOL C8 8 0.0 13.019 9 CH1R6 1 CHOL C9 9 0.0 13.019 10 CH0* 1 CHOL C10 10 0.0 12.011 11 CH2R6 1 CHOL C11 11 0.0 14.027 12 CH2R6 1 CHOL C12 12 0.0 14.027 13 CH0* 1 CHOL C13 13 0.0 12.011 14 CH1R6 1 CHOL C14 14 0.0 13.019 15 CH2R5 1 CHOL C15 15 0.0 14.027 16 CH2R5 1 CHOL C16 16 0.0 14.027 17 CH1R5 1 CHOL C17 17 0.0 13.019 18 CH3* 1 CHOL C18 18 0.0 15.035 19 CH3* 1 CHOL C19 19 0.0 15.035 20 CH1* 1 CHOL C20 20 0.0 13.019 21 CH3* 1 CHOL C21 20 0.0 15.035 22 CH2* 1 CHOL C22 20 0.0 14.027 23 CH2* 1 CHOL C23 21 0.0 14.027 24 CH2* 1 CHOL C24 21 0.0 14.027 25 CH1* 1 CHOL C25 22 0.0 13.019 26 CH3* 1 CHOL C26 22 0.0 15.035 27 CH3* 1 CHOL C27 22 0.0 15.035 28 OA 1 CHOL O28 23 -0.675 15.9994 29 H 1 CHOL H29 24 0.405 1.008 [ bonds ] ; ai aj funct c0 c1 c2 c3 1 2 2 gb_26 1 10 2 gb_26 2 3 2 gb_26 3 4 2 gb_26 4 5 2 gb_58a 5 6 2 gb_57 5 10 2 gb_58a 6 7 2 gb_58a 7 8 2 gb_26 8 9 2 gb_26 8 14 2 gb_26 9 10 2 gb_26 9 11 2 gb_26 10 19 2 gb_26 11 12 2 gb_26 12 13 2 gb_26 13 14 2 gb_61 13 17 2 gb_60 13 18 2 gb_26 14 15 2 gb_60 15 16 2 gb_60 16 17 2 gb_60 17 20 2 gb_26 20 21 2 gb_26 20 22 2 gb_26 22 23 2 gb_26 23 24 2 gb_26 24 25 2 gb_26 25 26 2 gb_26 25 27 2 gb_26 3 28 2 gb_17 28 29 2 gb_1 [ pairs ] 1 4 1 2 5 1 3 10 1 ;5 8 1 ;6 9 1 7 10 1 8 12 1 9 13 1 11 14 1 18 11 1 18 8 1 18 15 1 18 16 1 19 2 1 19 4 1 19 6 1 19 8 1 19 11 1 20 15 1 28 1 1 28 5 1 ; 12 20 1 13 21 1 13 22 1 14 20 1 15 20 1 16 21 1 16 21 1 16 22 1 17 23 1 18 20 1 20 24 1 21 23 1 22 25 1 23 26 1 23 27 1 [ angles ] 1 2 3 2 ga_14 1 10 5 2 ga_12 1 10 9 2 ga_12 1 10 19 2 ga_12 2 1 10 2 ga_14 2 3 4 2 ga_12 3 4 5 2 ga_14 4 5 6 2 ga_55 4 5 10 2 ga_49 5 6 7 2 ga_55 5 10 9 2 ga_12 5 10 19 2 ga_12 6 5 10 2 ga_55 6 7 8 2 ga_14 7 8 9 2 ga_12 7 8 14 2 ga_12 8 9 10 2 ga_12 8 9 11 2 ga_12 8 14 13 2 ga_12 8 14 15 2 ga_12 9 10 19 2 ga_12 10 9 11 2 ga_12 11 12 13 2 ga_14 12 13 14 2 ga_12 12 13 17 2 ga_12 12 13 18 2 ga_12 13 14 15 2 ga_54 13 17 16 2 ga_54 13 17 20 2 ga_12 14 13 17 2 ga_54 14 13 18 2 ga_12 14 15 16 2 ga_54 15 16 17 2 ga_54 16 17 20 2 ga_12 17 13 18 2 ga_12 17 20 21 2 ga_12 17 20 22 2 ga_12 20 22 23 2 ga_14 21 20 22 2 ga_12 22 23 24 2 ga_14 23 24 25 2 ga_14 24 25 26 2 ga_12 24 25 27 2 ga_12 26 25 27 2 ga_12 3 28 29 2 ga_11 2 3 28 2 ga_12 4 3 28 2 ga_12 [ dihedrals ] 1 2 3 4 3 gd_swc20 2 3 4 5 3 gd_swc20 ;3 4 5 10 3 gd_swc20 3 4 5 6 3 gd_kw4a1 4 5 10 9 3 gd_swc20 2 1 10 9 3 gd_swc20 10 1 2 3 3 gd_swc20 ; 4 5 6 7 1 gd_5 5 6 7 8 3 gd_kw34a1 6 7 8 9 3 gd_kw4a1 7 8 9 11 3 gd_swc20 8 9 10 1 3 gd_swc20 ; 10 9 11 12 3 gd_swc20 9 11 12 13 3 gd_swc20 11 12 13 17 3 gd_swc20 12 13 14 15 3 gd_swc20 13 14 8 7 3 gd_swc20 ; 8 14 15 16 3 gd_swc20 ; 14 15 16 17 3 gd_swc20 15 16 17 20 3 gd_swc20 16 17 13 12 3 gd_swc20 ; 16 17 20 21 3 gd_swc20 17 20 22 23 3 gd_swc20 20 22 23 24 3 gd_swc20 22 23 24 25 1 gd_17c 23 24 25 26 3 gd_swc20 ; 4 3 28 29 1 gd_13 [ dihedrals ] 10 5 6 7 2 gi_1 14 15 16 17 2 gi_1a 8 14 7 9 2 gi_2 9 11 10 8 2 gi_2 14 8 15 13 2 gi_2 17 20 13 16 2 gi_2 20 17 21 22 2 gi_2 3 4 2 28 2 gi_2 5534