* \\\\\\\ CHARMM27 All-Hydrogen Lipid Topology File /////// * \\\\\\\\\\\\\\\\\\ Developmental ///////////////////////// * POPG topology and parameters by Hyunbum Jang * found in a 22 1 file (named top_all27_prot_lipid_hgj.inp) * 27 1 ! atomtypes from Charmm 27 MASS 1 HL 1.008000 H ! polar H (equivalent to protein H) MASS 2 HCL 1.008000 H ! charged H for PE (equivalent to protein HC) MASS 3 HT 1.008000 H ! TIPS3P WATER HYDROGEN MASS 4 HOL 1.008000 H ! Nucleic acid phosphate hydroxyl proton MASS 5 HAL1 1.008000 H ! alphatic proton MASS 6 HAL2 1.008000 H ! alphatic proton MASS 7 HAL3 1.008000 H ! alphatic proton MASS 8 HEL1 1.008000 H ! for alkene; RHC=CR MASS 9 HEL2 1.008000 H ! for alkene; H2C=CR MASS 20 CL 12.011000 C ! carbonyl C (acetic acid/methyl acetate) MASS 21 CTL1 12.011000 C ! sp3 carbon with 1 H (-CH1-) MASS 22 CTL2 12.011000 C ! carbon of methylene group (-CH2-) MASS 23 CTL3 12.011000 C ! carbon of methyl group (-CH3) MASS 24 CTL5 12.011000 C ! carbon of methyl group (-CH3) for tetramethylammonium MASS 25 CEL1 12.011000 C ! for alkene; RHC=CR MASS 26 CEL2 12.011000 C ! for alkene; H2C=CR MASS 40 NTL 14.007000 N ! ammonium nitrogen MASS 41 NH3L 14.007000 N ! nitrogen phosphatidylethanolamine MASS 60 OBL 15.999400 O ! acetic acid carboxyl oxygen (e. to protein OB) MASS 61 OCL 15.999400 O ! acetate oxygen MASS 62 OT 15.999400 O ! TIPS3P WATER OXYGEN MASS 63 OSL 15.999400 O ! Nucleic acid phosphate ester oxygen MASS 64 O2L 15.999400 O ! Nucleic acid =O in phosphate or sulfate MASS 65 OHL 15.999400 O ! Nucleic acid phosphate hydroxyl oxygen MASS 80 PL 30.974000 P ! phosphorus MASS 85 SL 32.060000 S ! Sulfate sulfur MASS 90 SOD 22.989770 NA ! Sodium Ion MASS 91 MG 24.305000 MG ! Magnesium Ion MASS 92 POT 39.102000 K ! Potassium Ion! check masses MASS 93 CES 132.900000 CS ! Cesium Ion MASS 94 CAL 40.080000 CA ! Calcium Ion MASS 95 CLA 35.450000 CL ! Chloride Ion MASS 96 ZN 65.370000 ZN ! zinc (II) cation MASS 99 DUM 0.000000 H ! dummy atom DEFA FIRS none LAST none AUTOGENERATE ANGLES DIHEDRALS RESI POPG -1.00 ! 1,2 palm-oleo-SN-glycero-3-Phosphatidylglycerol ! (Hyunbum Jang) ! (OB:changed HAL -> HAL1, HAL2 for use with par_all27_lipid.prm) ! Polar Head and glycerol backbone GROUP ATOM CG3 CTL2 0.05 ! ATOM HG31 HAL2 0.09 ! HG32 ATOM HG32 HAL2 0.09 ! | ATOM OG3 OHL -0.66 ! HG31--CG3--OG3-HO3 ATOM HO3 HOL 0.43 ! | ATOM CG2 CTL1 0.14 ! | alpha6 ATOM HG21 HAL1 0.09 ! | ATOM OG2 OHL -0.66 ! HG21--CG2--OG2-HO2 ATOM HO2 HOL 0.43 ! | GROUP ! | alpha5 ATOM CG1 CTL2 -0.08 ! | ATOM HG11 HAL2 0.09 ! HG11--CG1---HG12 ATOM HG12 HAL2 0.09 ! | alpha4 ATOM P PL 1.50 ! O13 O12 ATOM O13 O2L -0.80 ! \\ / alpha3 ATOM O14 O2L -0.80 ! (-) P ATOM O11 OSL -0.55 ! // \ alpha2 ATOM O12 OSL -0.55 ! O14 O11 ATOM C1 CTL2 -0.08 ! | alpha1 ATOM HA HAL2 0.09 ! HA---C1---HB ATOM HB HAL2 0.09 ! | theta1 GROUP ! | ATOM C2 CTL1 0.04 ! HS---C2-------------- ATOM HS HAL1 0.09 ! | beta1 | ATOM O21 OSL -0.34 ! O22 O21 theta3 ATOM C21 CL 0.63 ! \\ / beta2 | ATOM O22 OBL -0.52 ! C21 | ATOM C22 CTL2 -0.08 ! | beta3 | ATOM H2R HAL2 0.09 ! H2R---C22---H2S | ATOM H2S HAL2 0.09 ! | | GROUP ! | beta4 | ATOM C3 CTL2 -0.05 ! | | ATOM HX HAL2 0.09 ! | HX---C3---HY ATOM HY HAL2 0.09 ! | | gamma1 ATOM O31 OSL -0.34 ! | O32 O31 ATOM C31 CL 0.63 ! | \\ / gamma2 ATOM O32 OBL -0.52 ! | C31 ATOM C32 CTL2 -0.08 ! | | gamma3 ATOM H2X HAL2 0.09 ! | H2X---C32---H2Y ATOM H2Y HAL2 0.09 ! | | GROUP ! | | gamma4 ATOM C23 CTL2 -0.18 ! | | ATOM H3R HAL2 0.09 ! H3R ---C23---H3S | ATOM H3S HAL2 0.09 ! | | GROUP ! | | ATOM C24 CTL2 -0.18 ! | | ATOM H4R HAL2 0.09 ! H4R ---C24---H4S | ATOM H4S HAL2 0.09 ! | | GROUP ! | | ATOM C25 CTL2 -0.18 ! | | ATOM H5R HAL2 0.09 ! H5R ---C25---H5S | ATOM H5S HAL2 0.09 ! | | GROUP ! | | ATOM C26 CTL2 -0.18 ! | | ATOM H6R HAL2 0.09 ! H6R ---C26---H6S | ATOM H6S HAL2 0.09 ! | | GROUP ! | | ATOM C27 CTL2 -0.18 ! | | ATOM H7R HAL2 0.09 ! H7R ---C27---H7S | ATOM H7S HAL2 0.09 ! | | GROUP ! | | ATOM C28 CTL2 -0.18 ! | | ATOM H8R HAL2 0.09 ! H8R ---C28---H8S | ATOM H8S HAL2 0.09 ! | | GROUP ! | | ATOM C29 CEL1 -0.15 ! | | ATOM H91 HEL1 0.15 ! H91 ---C29 | GROUP ! || (CIS) | ATOM C210 CEL1 -0.15 ! || | ATOM H101 HEL1 0.15 ! H101---C210 | GROUP ! | | ATOM C211 CTL2 -0.18 ! | | ATOM H11R HAL2 0.09 ! H11R---C211--H11S | ATOM H11S HAL2 0.09 ! | | GROUP ! | | ATOM C212 CTL2 -0.18 ! | | ATOM H12R HAL2 0.09 ! H12R---C212--H12S | ATOM H12S HAL2 0.09 ! | | GROUP ! | | ATOM C213 CTL2 -0.18 ! | | ATOM H13R HAL2 0.09 ! H13R---C213--H13S | ATOM H13S HAL2 0.09 ! | | GROUP ! | | ATOM C214 CTL2 -0.18 ! | | ATOM H14R HAL2 0.09 ! H14R---C214--H14S | ATOM H14S HAL2 0.09 ! | | GROUP ! | | ATOM C215 CTL2 -0.18 ! | | ATOM H15R HAL2 0.09 ! H15R---C215--H15S | ATOM H15S HAL2 0.09 ! | | GROUP ! | | ATOM C216 CTL2 -0.18 ! | | ATOM H16R HAL2 0.09 ! H16R---C216--H16S | ATOM H16S HAL2 0.09 ! | | GROUP ! | | ATOM C217 CTL2 -0.18 ! | | ATOM H17R HAL2 0.09 ! H17R---C217--H17S | ATOM H17S HAL2 0.09 ! | | GROUP ! | | ATOM C218 CTL3 -0.27 ! | | ATOM H18R HAL3 0.09 ! H18R---C218--H18S | ATOM H18S HAL3 0.09 ! | | ATOM H18T HAL3 0.09 ! H18T | GROUP ! | ATOM C33 CTL2 -0.18 ! | ATOM H3X HAL2 0.09 ! H3X ---C33---H3Y ATOM H3Y HAL2 0.09 ! | GROUP ! | ATOM C34 CTL2 -0.18 ! | ATOM H4X HAL2 0.09 ! H4X ---C34---H4Y ATOM H4Y HAL2 0.09 ! | GROUP ! | ATOM C35 CTL2 -0.18 ! | ATOM H5X HAL2 0.09 ! H5X ---C35---H5Y ATOM H5Y HAL2 0.09 ! | GROUP ! | ATOM C36 CTL2 -0.18 ! | ATOM H6X HAL2 0.09 ! H6X ---C36---H6Y ATOM H6Y HAL2 0.09 ! | GROUP ! | ATOM C37 CTL2 -0.18 ! | ATOM H7X HAL2 0.09 ! H7X ---C37---H7Y ATOM H7Y HAL2 0.09 ! | GROUP ! | ATOM C38 CTL2 -0.18 ! | ATOM H8X HAL2 0.09 ! H8X ---C38---H8Y ATOM H8Y HAL2 0.09 ! | GROUP ! | ATOM C39 CTL2 -0.18 ! | ATOM H9X HAL2 0.09 ! H9X ---C39---H9Y ATOM H9Y HAL2 0.09 ! | GROUP ! | ATOM C310 CTL2 -0.18 ! | ATOM H10X HAL2 0.09 ! H10X---C310--H10Y ATOM H10Y HAL2 0.09 ! | GROUP ! | ATOM C311 CTL2 -0.18 ! | ATOM H11X HAL2 0.09 ! H11X---C311--H11Y ATOM H11Y HAL2 0.09 ! | GROUP ! | ATOM C312 CTL2 -0.18 ! | ATOM H12X HAL2 0.09 ! H12X---C312--H12Y ATOM H12Y HAL2 0.09 ! | GROUP ! | ATOM C313 CTL2 -0.18 ! | ATOM H13X HAL2 0.09 ! H13X---C313--H13Y ATOM H13Y HAL2 0.09 ! | GROUP ! | ATOM C314 CTL2 -0.18 ! | ATOM H14X HAL2 0.09 ! H14X---C314--H14Y ATOM H14Y HAL2 0.09 ! | GROUP ! | ATOM C315 CTL2 -0.18 ! | ATOM H15X HAL2 0.09 ! H15X---C315--H15Y ATOM H15Y HAL2 0.09 ! | GROUP ! | ATOM C316 CTL3 -0.27 ! | ATOM H16X HAL3 0.09 ! H16X---C316--H16Y ATOM H16Y HAL3 0.09 ! | ATOM H16Z HAL3 0.09 ! H16Z !BONDING FROM PG BOND CG3 CG2 CG3 HG31 CG3 HG32 CG3 OG3 OG3 HO3 BOND CG2 CG1 CG2 HG21 CG2 OG2 OG2 HO2 BOND CG1 O12 CG1 HG11 CG1 HG12 BOND O12 P P O11 P O13 P O14 ! Glycerol Backbone BOND C1 HA C1 HB C1 C2 C1 O11 BOND C2 HS C2 C3 C2 O21 BOND C3 HX C3 HY C3 O31 ! Chain from C2 BOND O21 C21 BOND C21 C22 DOUBLE C21 O22 BOND C22 H2R C22 H2S C22 C23 BOND C23 H3R C23 H3S C23 C24 BOND C24 H4R C24 H4S C24 C25 BOND C25 H5R C25 H5S C25 C26 BOND C26 H6R C26 H6S C26 C27 BOND C27 H7R C27 H7S C27 C28 BOND C28 H8R C28 H8S C28 C29 BOND C29 H91 DOUBLE C29 C210 BOND C210 H101 C210 C211 BOND C211 H11R C211 H11S C211 C212 BOND C212 H12R C212 H12S C212 C213 BOND C213 H13R C213 H13S C213 C214 BOND C214 H14R C214 H14S C214 C215 BOND C215 H15R C215 H15S C215 C216 BOND C216 H16R C216 H16S C216 C217 BOND C217 H17R C217 H17S C217 C218 BOND C218 H18R C218 H18S C218 H18T ! Chain From C3 BOND O31 C31 BOND C31 C32 DOUBLE C31 O32 BOND C32 H2X C32 H2Y C32 C33 BOND C33 H3X C33 H3Y C33 C34 BOND C34 H4X C34 H4Y C34 C35 BOND C35 H5X C35 H5Y C35 C36 BOND C36 H6X C36 H6Y C36 C37 BOND C37 H7X C37 H7Y C37 C38 BOND C38 H8X C38 H8Y C38 C39 BOND C39 H9X C39 H9Y C39 C310 BOND C310 H10X C310 H10Y C310 C311 BOND C311 H11X C311 H11Y C311 C312 BOND C312 H12X C312 H12Y C312 C313 BOND C313 H13X C313 H13Y C313 C314 BOND C314 H14X C314 H14Y C314 C315 BOND C315 H15X C315 H15Y C315 C316 BOND C316 H16X C316 H16Y C316 H16Z IMPR C21 O21 C22 O22 C31 O31 C32 O32 !IC table from IC generate, geometry is guessed ! Polar head (angle names from Sundaralingam) IC C2 C1 O11 P 0.0 0.0 180.0 0.0 0.0 !alpha1 IC C1 O11 P O12 0.0 0.0 180.0 0.0 0.0 !alpha2 IC O11 O12 *P O13 0.0 0.0 120.0 0.0 0.0 IC O11 O12 *P O14 0.0 0.0 240.0 0.0 0.0 IC O11 P O12 CG1 0.0 0.0 180.0 0.0 0.0 !alpha3 IC O12 CG2 *CG1 HG11 0.0 0.0 120.0 0.0 0.0 IC O12 CG2 *CG1 HG12 0.0 0.0 240.0 0.0 0.0 IC P O12 CG1 CG2 0.0 0.0 180.0 0.0 0.0 !alpha4 IC O12 CG1 CG2 CG3 0.0 0.0 0.0 0.0 0.0 ! t1 IC O12 CG1 CG2 OG2 0.0 0.0 0.0 0.0 0.0 ! t2 IC CG1 CG2 CG3 OG3 0.0 0.0 0.0 0.0 0.0 ! t3 IC OG2 CG2 CG3 OG3 0.0 0.0 0.0 0.0 0.0 ! t3 ! Glycerol IC O11 C1 C2 C3 0.0 0.0 120.0 0.0 0.0 !theta1 IC C1 C2 C3 O31 0.0 0.0 180.0 0.0 0.0 !theta3 IC C1 C3 *C2 O21 0.0 0.0 -120.0 0.0 0.0 ! for stereo-specific phopholipid at carbon C2 (labeled hydrogen S) IC O11 C2 *C1 HA 0.0 0.0 +120.0 0.0 0.0 IC O11 C2 *C1 HB 0.0 0.0 -120.0 0.0 0.0 IC O21 C1 *C2 HS 0.0 0.0 +120.0 0.0 0.0 IC O31 C2 *C3 HX 0.0 0.0 +120.0 0.0 0.0 IC O31 C2 *C3 HY 0.0 0.0 -120.0 0.0 0.0 ! Chain 1 IC C1 C2 O21 C21 0.0 0.0 180.0 0.0 0.0 !beta1 IC C2 O21 C21 C22 0.0 0.0 120.0 0.0 0.0 !beta2 IC O21 C21 C22 C23 0.0 0.0 180.0 0.0 0.0 !beta3 IC C22 O21 *C21 O22 0.0 0.0 180.0 0.0 0.0 IC C21 C22 C23 C24 0.0 0.0 180.0 0.0 0.0 !beta4 IC C22 C23 C24 C25 0.0 0.0 180.0 0.0 0.0 !beta5 IC C23 C24 C25 C26 0.0 0.0 180.0 0.0 0.0 !beta6 IC C24 C25 C26 C27 0.0 0.0 180.0 0.0 0.0 !beta7 IC C25 C26 C27 C28 0.0 0.0 180.0 0.0 0.0 !beta8 IC C26 C27 C28 C29 0.0 0.0 180.0 0.0 0.0 !beta9 IC C27 C28 C29 C210 0.0 0.0 180.0 0.0 0.0 !beta10 IC C28 C29 C210 C211 0.0 0.0 180.0 0.0 0.0 !beta11 IC C29 C210 C211 C212 0.0 0.0 180.0 0.0 0.0 !beta12 IC C210 C211 C212 C213 0.0 0.0 180.0 0.0 0.0 !beta13 IC C211 C212 C213 C214 0.0 0.0 180.0 0.0 0.0 !beta14 IC C212 C213 C214 C215 0.0 0.0 180.0 0.0 0.0 !beta15 IC C213 C214 C215 C216 0.0 0.0 180.0 0.0 0.0 !beta16 IC C214 C215 C216 C217 0.0 0.0 180.0 0.0 0.0 !beta17 IC C215 C216 C217 C218 0.0 0.0 180.0 0.0 0.0 !beta18 ! Chain 2 IC C2 C3 O31 C31 0.0 0.0 -120.0 0.0 0.0 !gamma1 IC C3 O31 C31 C32 0.0 0.0 180.0 0.0 0.0 !gamma2 IC O31 C31 C32 C33 0.0 0.0 180.0 0.0 0.0 !gamma3 IC C32 O31 *C31 O32 0.0 0.0 180.0 0.0 0.0 IC C31 C32 C33 C34 0.0 0.0 180.0 0.0 0.0 !gamma4 IC C32 C33 C34 C35 0.0 0.0 180.0 0.0 0.0 !gamma5 IC C33 C34 C35 C36 0.0 0.0 180.0 0.0 0.0 !gamma6 IC C34 C35 C36 C37 0.0 0.0 180.0 0.0 0.0 !gamma7 IC C35 C36 C37 C38 0.0 0.0 180.0 0.0 0.0 !gamma8 IC C36 C37 C38 C39 0.0 0.0 180.0 0.0 0.0 !gamma9 IC C37 C38 C39 C310 0.0 0.0 180.0 0.0 0.0 !gamma10 IC C38 C39 C310 C311 0.0 0.0 180.0 0.0 0.0 !gamma11 IC C39 C310 C311 C312 0.0 0.0 180.0 0.0 0.0 !gamma12 IC C310 C311 C312 C313 0.0 0.0 180.0 0.0 0.0 !gamma13 IC C311 C312 C313 C314 0.0 0.0 180.0 0.0 0.0 !gamma14 IC C312 C313 C314 C315 0.0 0.0 180.0 0.0 0.0 !gamma14 IC C313 C314 C315 C316 0.0 0.0 180.0 0.0 0.0 !gamma14