diff options
Diffstat (limited to 'sci-chemistry/ambertools/files/ambertools-15-update.4.patch')
| -rw-r--r-- | sci-chemistry/ambertools/files/ambertools-15-update.4.patch | 908 |
1 files changed, 0 insertions, 908 deletions
diff --git a/sci-chemistry/ambertools/files/ambertools-15-update.4.patch b/sci-chemistry/ambertools/files/ambertools-15-update.4.patch deleted file mode 100644 index 4176a583a..000000000 --- a/sci-chemistry/ambertools/files/ambertools-15-update.4.patch +++ /dev/null @@ -1,908 +0,0 @@ -*******> update.4 -Author: Benjamin D. Madej -Date: October 19, 2015 -Programs: Leap, Lipid14 force field -Description: Adds a parameter set for cholesterol to the Lipid14 force field. - Please reference: - Madej, B. D.; Gould, I.R.; Walker, R. C. A Parameterization of - Cholesterol for Mixed Lipid Bilayer Simulation within the Amber - Lipid14 Force Field. J. Phys. Chem. B 2015, 119 (38) - pp 12424-12435. -------------------------------------------------------------------------------- - dat/leap/lib/lipid14.lib | 480 ++++++++++++++++++++++++++++++++++++++++++++++ - dat/leap/parm/lipid11.dat | 2 +- - dat/leap/parm/lipid14.dat | 291 ++++++++++++++++++---------- - 3 files changed, 666 insertions(+), 107 deletions(-) - -diff --git dat/leap/lib/lipid14.lib dat/leap/lib/lipid14.lib -index 891937b..75c2f2b 100644 ---- dat/leap/lib/lipid14.lib -+++ dat/leap/lib/lipid14.lib -@@ -1,10 +1,490 @@ - !!index array str -+ "CHL" - "LA" - "MY" - "OL" - "PA" - "PC" - "PE" -+!entry.CHL.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg -+ "C1" "cA" 0 1 131073 1 6 -0.031691 -+ "H11" "hA" 0 1 131073 2 1 0.009380 -+ "H12" "hA" 0 1 131073 3 1 0.009380 -+ "C2" "cA" 0 1 131073 4 6 -0.088130 -+ "H21" "hA" 0 1 131073 5 1 0.044625 -+ "H22" "hA" 0 1 131073 6 1 0.044625 -+ "C3" "cA" 0 1 131073 7 6 0.293553 -+ "H31" "hE" 0 1 131073 8 1 0.029611 -+ "C4" "cA" 0 1 131073 9 6 -0.162218 -+ "H41" "hA" 0 1 131073 10 1 0.090036 -+ "H42" "hA" 0 1 131073 11 1 0.090036 -+ "C5" "cB" 0 1 131073 12 6 -0.139495 -+ "C6" "cB" 0 1 131073 13 6 -0.208190 -+ "H61" "hB" 0 1 131073 14 1 0.122828 -+ "C7" "cA" 0 1 131073 15 6 -0.069897 -+ "H71" "hA" 0 1 131073 16 1 0.047919 -+ "H72" "hA" 0 1 131073 17 1 0.047919 -+ "C8" "cA" 0 1 131073 18 6 -0.011390 -+ "H81" "hA" 0 1 131073 19 1 0.072891 -+ "C9" "cA" 0 1 131073 20 6 0.019609 -+ "H91" "hA" 0 1 131073 21 1 0.029289 -+ "C10" "cA" 0 1 131073 22 6 0.079112 -+ "C11" "cA" 0 1 131073 23 6 -0.066365 -+ "H111" "hA" 0 1 131073 24 1 0.030085 -+ "H112" "hA" 0 1 131073 25 1 0.030085 -+ "C12" "cA" 0 1 131073 26 6 -0.064973 -+ "H121" "hA" 0 1 131073 27 1 0.010352 -+ "H122" "hA" 0 1 131073 28 1 0.010352 -+ "C13" "cA" 0 1 131073 29 6 0.057407 -+ "C14" "cA" 0 1 131073 30 6 0.005830 -+ "H141" "hA" 0 1 131073 31 1 0.031557 -+ "C15" "cA" 0 1 131073 32 6 -0.101977 -+ "H151" "hA" 0 1 131073 33 1 0.026458 -+ "H152" "hA" 0 1 131073 34 1 0.026458 -+ "C16" "cA" 0 1 131073 35 6 -0.092064 -+ "H161" "hA" 0 1 131073 36 1 0.033335 -+ "H162" "hA" 0 1 131073 37 1 0.033335 -+ "C17" "cA" 0 1 131073 38 6 0.032398 -+ "H171" "hA" 0 1 131073 39 1 0.016590 -+ "C18" "cA" 0 1 131073 40 6 -0.115049 -+ "H181" "hA" 0 1 131073 41 1 0.024541 -+ "H182" "hA" 0 1 131073 42 1 0.024541 -+ "H183" "hA" 0 1 131073 43 1 0.024541 -+ "C19" "cA" 0 1 131073 44 6 -0.108064 -+ "H191" "hA" 0 1 131073 45 1 0.033990 -+ "H192" "hA" 0 1 131073 46 1 0.033990 -+ "H193" "hA" 0 1 131073 47 1 0.033990 -+ "C20" "cD" 0 1 131075 48 6 0.044268 -+ "H201" "hL" 0 1 131075 49 1 0.020951 -+ "C21" "cD" 0 1 131075 50 6 -0.154621 -+ "H211" "hL" 0 1 131075 51 1 0.036274 -+ "H212" "hL" 0 1 131075 52 1 0.036274 -+ "H213" "hL" 0 1 131075 53 1 0.036274 -+ "C22" "cD" 0 1 131075 54 6 -0.039033 -+ "H221" "hL" 0 1 131075 55 1 0.008359 -+ "H222" "hL" 0 1 131075 56 1 0.008359 -+ "C23" "cD" 0 1 131075 57 6 -0.028460 -+ "H231" "hL" 0 1 131075 58 1 0.015742 -+ "H232" "hL" 0 1 131075 59 1 0.015742 -+ "C24" "cD" 0 1 131075 60 6 -0.125596 -+ "H241" "hL" 0 1 131075 61 1 0.040110 -+ "H242" "hL" 0 1 131075 62 1 0.040110 -+ "C25" "cD" 0 1 131075 63 6 0.212446 -+ "H251" "hL" 0 1 131075 64 1 -0.002466 -+ "C26" "cD" 0 1 131075 65 6 -0.257776 -+ "H261" "hL" 0 1 131075 66 1 0.057982 -+ "H262" "hL" 0 1 131075 67 1 0.057982 -+ "H263" "hL" 0 1 131075 68 1 0.057982 -+ "C27" "cD" 0 1 131075 69 6 -0.257776 -+ "H271" "hL" 0 1 131075 70 1 0.057982 -+ "H272" "hL" 0 1 131075 71 1 0.057982 -+ "H273" "hL" 0 1 131075 72 1 0.057982 -+ "O1" "oH" 0 1 131073 73 8 -0.703022 -+ "HO1" "hO" 0 1 131073 74 1 0.414804 -+!entry.CHL.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg -+ "C1" "cA" 0 -1 0.0 -+ "H11" "hA" 0 -1 0.0 -+ "H12" "hA" 0 -1 0.0 -+ "C2" "cA" 0 -1 0.0 -+ "H21" "hA" 0 -1 0.0 -+ "H22" "hA" 0 -1 0.0 -+ "C3" "cA" 0 -1 0.0 -+ "H31" "hE" 0 -1 0.0 -+ "C4" "cA" 0 -1 0.0 -+ "H41" "hA" 0 -1 0.0 -+ "H42" "hA" 0 -1 0.0 -+ "C5" "cB" 0 -1 0.0 -+ "C6" "cB" 0 -1 0.0 -+ "H61" "hB" 0 -1 0.0 -+ "C7" "cA" 0 -1 0.0 -+ "H71" "hA" 0 -1 0.0 -+ "H72" "hA" 0 -1 0.0 -+ "C8" "cA" 0 -1 0.0 -+ "H81" "hA" 0 -1 0.0 -+ "C9" "cA" 0 -1 0.0 -+ "H91" "hA" 0 -1 0.0 -+ "C10" "cA" 0 -1 0.0 -+ "C11" "cA" 0 -1 0.0 -+ "H111" "hA" 0 -1 0.0 -+ "H112" "hA" 0 -1 0.0 -+ "C12" "cA" 0 -1 0.0 -+ "H121" "hA" 0 -1 0.0 -+ "H122" "hA" 0 -1 0.0 -+ "C13" "cA" 0 -1 0.0 -+ "C14" "cA" 0 -1 0.0 -+ "H141" "hA" 0 -1 0.0 -+ "C15" "cA" 0 -1 0.0 -+ "H151" "hA" 0 -1 0.0 -+ "H152" "hA" 0 -1 0.0 -+ "C16" "cA" 0 -1 0.0 -+ "H161" "hA" 0 -1 0.0 -+ "H162" "hA" 0 -1 0.0 -+ "C17" "cA" 0 -1 0.0 -+ "H171" "hA" 0 -1 0.0 -+ "C18" "cA" 0 -1 0.0 -+ "H181" "hA" 0 -1 0.0 -+ "H182" "hA" 0 -1 0.0 -+ "H183" "hA" 0 -1 0.0 -+ "C19" "cA" 0 -1 0.0 -+ "H191" "hA" 0 -1 0.0 -+ "H192" "hA" 0 -1 0.0 -+ "H193" "hA" 0 -1 0.0 -+ "C20" "cA" 0 -1 0.0 -+ "H201" "hA" 0 -1 0.0 -+ "C21" "cA" 0 -1 0.0 -+ "H211" "hA" 0 -1 0.0 -+ "H212" "hA" 0 -1 0.0 -+ "H213" "hA" 0 -1 0.0 -+ "C22" "cA" 0 -1 0.0 -+ "H221" "hA" 0 -1 0.0 -+ "H222" "hA" 0 -1 0.0 -+ "C23" "cA" 0 -1 0.0 -+ "H231" "hA" 0 -1 0.0 -+ "H232" "hA" 0 -1 0.0 -+ "C24" "cA" 0 -1 0.0 -+ "H241" "hA" 0 -1 0.0 -+ "H242" "hA" 0 -1 0.0 -+ "C25" "cA" 0 -1 0.0 -+ "H251" "hA" 0 -1 0.0 -+ "C26" "cA" 0 -1 0.0 -+ "H261" "hA" 0 -1 0.0 -+ "H262" "hA" 0 -1 0.0 -+ "H263" "hA" 0 -1 0.0 -+ "C27" "cA" 0 -1 0.0 -+ "H271" "hA" 0 -1 0.0 -+ "H272" "hA" 0 -1 0.0 -+ "H273" "hA" 0 -1 0.0 -+ "O1" "oH" 0 -1 0.0 -+ "HO1" "hO" 0 -1 0.0 -+!entry.CHL.unit.boundbox array dbl -+ -1.000000 -+ 0.0 -+ 0.0 -+ 0.0 -+ 0.0 -+!entry.CHL.unit.childsequence single int -+ 2 -+!entry.CHL.unit.connect array int -+ 0 -+ 0 -+!entry.CHL.unit.connectivity table int atom1x int atom2x int flags -+ 1 2 1 -+ 1 3 1 -+ 1 4 1 -+ 1 22 1 -+ 4 5 1 -+ 4 6 1 -+ 4 7 1 -+ 7 8 1 -+ 7 9 1 -+ 7 73 1 -+ 9 10 1 -+ 9 11 1 -+ 9 12 1 -+ 12 13 2 -+ 12 22 1 -+ 13 14 1 -+ 13 15 1 -+ 15 16 1 -+ 15 17 1 -+ 15 18 1 -+ 18 19 1 -+ 18 20 1 -+ 18 30 1 -+ 20 21 1 -+ 20 22 1 -+ 20 23 1 -+ 22 44 1 -+ 23 24 1 -+ 23 25 1 -+ 23 26 1 -+ 26 27 1 -+ 26 28 1 -+ 26 29 1 -+ 29 30 1 -+ 29 38 1 -+ 29 40 1 -+ 30 31 1 -+ 30 32 1 -+ 32 33 1 -+ 32 34 1 -+ 32 35 1 -+ 35 36 1 -+ 35 37 1 -+ 35 38 1 -+ 38 39 1 -+ 38 48 1 -+ 40 41 1 -+ 40 42 1 -+ 40 43 1 -+ 44 45 1 -+ 44 46 1 -+ 44 47 1 -+ 48 49 1 -+ 48 50 1 -+ 48 54 1 -+ 50 51 1 -+ 50 52 1 -+ 50 53 1 -+ 54 55 1 -+ 54 56 1 -+ 54 57 1 -+ 57 58 1 -+ 57 59 1 -+ 57 60 1 -+ 60 61 1 -+ 60 62 1 -+ 60 63 1 -+ 63 64 1 -+ 63 65 1 -+ 63 69 1 -+ 65 66 1 -+ 65 67 1 -+ 65 68 1 -+ 69 70 1 -+ 69 71 1 -+ 69 72 1 -+ 73 74 1 -+!entry.CHL.unit.hierarchy table str abovetype int abovex str belowtype int belowx -+ "U" 0 "R" 1 -+ "R" 1 "A" 1 -+ "R" 1 "A" 2 -+ "R" 1 "A" 3 -+ "R" 1 "A" 4 -+ "R" 1 "A" 5 -+ "R" 1 "A" 6 -+ "R" 1 "A" 7 -+ "R" 1 "A" 8 -+ "R" 1 "A" 9 -+ "R" 1 "A" 10 -+ "R" 1 "A" 11 -+ "R" 1 "A" 12 -+ "R" 1 "A" 13 -+ "R" 1 "A" 14 -+ "R" 1 "A" 15 -+ "R" 1 "A" 16 -+ "R" 1 "A" 17 -+ "R" 1 "A" 18 -+ "R" 1 "A" 19 -+ "R" 1 "A" 20 -+ "R" 1 "A" 21 -+ "R" 1 "A" 22 -+ "R" 1 "A" 23 -+ "R" 1 "A" 24 -+ "R" 1 "A" 25 -+ "R" 1 "A" 26 -+ "R" 1 "A" 27 -+ "R" 1 "A" 28 -+ "R" 1 "A" 29 -+ "R" 1 "A" 30 -+ "R" 1 "A" 31 -+ "R" 1 "A" 32 -+ "R" 1 "A" 33 -+ "R" 1 "A" 34 -+ "R" 1 "A" 35 -+ "R" 1 "A" 36 -+ "R" 1 "A" 37 -+ "R" 1 "A" 38 -+ "R" 1 "A" 39 -+ "R" 1 "A" 40 -+ "R" 1 "A" 41 -+ "R" 1 "A" 42 -+ "R" 1 "A" 43 -+ "R" 1 "A" 44 -+ "R" 1 "A" 45 -+ "R" 1 "A" 46 -+ "R" 1 "A" 47 -+ "R" 1 "A" 48 -+ "R" 1 "A" 49 -+ "R" 1 "A" 50 -+ "R" 1 "A" 51 -+ "R" 1 "A" 52 -+ "R" 1 "A" 53 -+ "R" 1 "A" 54 -+ "R" 1 "A" 55 -+ "R" 1 "A" 56 -+ "R" 1 "A" 57 -+ "R" 1 "A" 58 -+ "R" 1 "A" 59 -+ "R" 1 "A" 60 -+ "R" 1 "A" 61 -+ "R" 1 "A" 62 -+ "R" 1 "A" 63 -+ "R" 1 "A" 64 -+ "R" 1 "A" 65 -+ "R" 1 "A" 66 -+ "R" 1 "A" 67 -+ "R" 1 "A" 68 -+ "R" 1 "A" 69 -+ "R" 1 "A" 70 -+ "R" 1 "A" 71 -+ "R" 1 "A" 72 -+ "R" 1 "A" 73 -+ "R" 1 "A" 74 -+!entry.CHL.unit.name single str -+ "CHL" -+!entry.CHL.unit.positions table dbl x dbl y dbl z -+ 4.697000 -1.469000 -0.739000 -+ 4.428000 -1.214000 -1.762000 -+ 4.303000 -2.462000 -0.556000 -+ 6.224000 -1.517000 -0.642000 -+ 6.547000 -1.874000 0.331000 -+ 6.617000 -2.214000 -1.376000 -+ 6.830000 -0.145000 -0.877000 -+ 6.590000 0.176000 -1.891000 -+ 6.246000 0.863000 0.111000 -+ 6.601000 0.589000 1.102000 -+ 6.636000 1.856000 -0.095000 -+ 4.731000 0.895000 0.070000 -+ 4.091000 2.041000 -0.088000 -+ 4.668000 2.946000 -0.204000 -+ 2.599000 2.206000 -0.119000 -+ 2.323000 3.070000 0.480000 -+ 2.290000 2.443000 -1.137000 -+ 1.853000 0.964000 0.375000 -+ 1.922000 0.946000 1.460000 -+ 2.514000 -0.306000 -0.204000 -+ 2.518000 -0.165000 -1.285000 -+ 4.012000 -0.452000 0.214000 -+ 1.671000 -1.566000 0.076000 -+ 2.085000 -2.410000 -0.467000 -+ 1.730000 -1.829000 1.125000 -+ 0.190000 -1.429000 -0.312000 -+ 0.108000 -1.322000 -1.392000 -+ -0.312000 -2.355000 -0.056000 -+ -0.469000 -0.212000 0.358000 -+ 0.381000 1.015000 -0.041000 -+ 0.381000 1.020000 -1.132000 -+ -0.462000 2.215000 0.391000 -+ -0.304000 2.443000 1.442000 -+ -0.217000 3.115000 -0.163000 -+ -1.913000 1.751000 0.131000 -+ -2.537000 1.930000 1.001000 -+ -2.357000 2.309000 -0.684000 -+ -1.859000 0.228000 -0.203000 -+ -1.794000 0.127000 -1.286000 -+ -0.546000 -0.407000 1.886000 -+ -1.062000 0.412000 2.374000 -+ 0.431000 -0.485000 2.344000 -+ -1.086000 -1.316000 2.130000 -+ 4.156000 -0.937000 1.675000 -+ 3.579000 -0.319000 2.354000 -+ 5.185000 -0.898000 2.008000 -+ 3.826000 -1.963000 1.788000 -+ -3.141000 -0.519000 0.237000 -+ -3.267000 -0.372000 1.309000 -+ -3.080000 -2.029000 -0.029000 -+ -2.330000 -2.520000 0.577000 -+ -2.851000 -2.232000 -1.072000 -+ -4.025000 -2.508000 0.198000 -+ -4.375000 0.093000 -0.461000 -+ -4.324000 1.175000 -0.403000 -+ -4.337000 -0.153000 -1.522000 -+ -5.732000 -0.335000 0.111000 -+ -5.862000 -1.406000 0.010000 -+ -5.752000 -0.121000 1.179000 -+ -6.898000 0.389000 -0.569000 -+ -6.718000 1.461000 -0.516000 -+ -6.910000 0.137000 -1.629000 -+ -8.286000 0.104000 0.028000 -+ -8.244000 0.333000 1.092000 -+ -8.705000 -1.362000 -0.122000 -+ -8.034000 -2.035000 0.400000 -+ -8.723000 -1.655000 -1.169000 -+ -9.702000 -1.521000 0.280000 -+ -9.336000 1.023000 -0.605000 -+ -9.079000 2.069000 -0.470000 -+ -10.316000 0.862000 -0.166000 -+ -9.420000 0.839000 -1.674000 -+ 8.224000 -0.262000 -0.734000 -+ 8.633000 0.570000 -0.924000 -+!entry.CHL.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x -+ 0 0 0 0 0 0 -+!entry.CHL.unit.residues table str name int seq int childseq int startatomx str restype int imagingx -+ "CHL" 1 75 1 "?" 0 -+!entry.CHL.unit.residuesPdbSequenceNumber array int -+ 0 -+!entry.CHL.unit.solventcap array dbl -+ -1.000000 -+ 0.0 -+ 0.0 -+ 0.0 -+ 0.0 -+!entry.CHL.unit.velocities table dbl x dbl y dbl z -+ 0.0 0.0 0.0 -+ 0.0 0.0 0.0 -+ 0.0 0.0 0.0 -+ 0.0 0.0 0.0 -+ 0.0 0.0 0.0 -+ 0.0 0.0 0.0 -+ 0.0 0.0 0.0 -+ 0.0 0.0 0.0 -+ 0.0 0.0 0.0 -+ 0.0 0.0 0.0 -+ 0.0 0.0 0.0 -+ 0.0 0.0 0.0 -+ 0.0 0.0 0.0 -+ 0.0 0.0 0.0 -+ 0.0 0.0 0.0 -+ 0.0 0.0 0.0 -+ 0.0 0.0 0.0 -+ 0.0 0.0 0.0 -+ 0.0 0.0 0.0 -+ 0.0 0.0 0.0 -+ 0.0 0.0 0.0 -+ 0.0 0.0 0.0 -+ 0.0 0.0 0.0 -+ 0.0 0.0 0.0 -+ 0.0 0.0 0.0 -+ 0.0 0.0 0.0 -+ 0.0 0.0 0.0 -+ 0.0 0.0 0.0 -+ 0.0 0.0 0.0 -+ 0.0 0.0 0.0 -+ 0.0 0.0 0.0 -+ 0.0 0.0 0.0 -+ 0.0 0.0 0.0 -+ 0.0 0.0 0.0 -+ 0.0 0.0 0.0 -+ 0.0 0.0 0.0 -+ 0.0 0.0 0.0 -+ 0.0 0.0 0.0 -+ 0.0 0.0 0.0 -+ 0.0 0.0 0.0 -+ 0.0 0.0 0.0 -+ 0.0 0.0 0.0 -+ 0.0 0.0 0.0 -+ 0.0 0.0 0.0 -+ 0.0 0.0 0.0 -+ 0.0 0.0 0.0 -+ 0.0 0.0 0.0 -+ 0.0 0.0 0.0 -+ 0.0 0.0 0.0 -+ 0.0 0.0 0.0 -+ 0.0 0.0 0.0 -+ 0.0 0.0 0.0 -+ 0.0 0.0 0.0 -+ 0.0 0.0 0.0 -+ 0.0 0.0 0.0 -+ 0.0 0.0 0.0 -+ 0.0 0.0 0.0 -+ 0.0 0.0 0.0 -+ 0.0 0.0 0.0 -+ 0.0 0.0 0.0 -+ 0.0 0.0 0.0 -+ 0.0 0.0 0.0 -+ 0.0 0.0 0.0 -+ 0.0 0.0 0.0 -+ 0.0 0.0 0.0 -+ 0.0 0.0 0.0 -+ 0.0 0.0 0.0 -+ 0.0 0.0 0.0 -+ 0.0 0.0 0.0 -+ 0.0 0.0 0.0 -+ 0.0 0.0 0.0 -+ 0.0 0.0 0.0 -+ 0.0 0.0 0.0 -+ 0.0 0.0 0.0 - !entry.LA.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg - "H12T" "hL" 0 1 131073 1 1 0.025809 - "C112" "cD" 0 1 131073 2 6 -0.118534 -diff --git dat/leap/parm/lipid11.dat dat/leap/parm/lipid11.dat -index 0f8d83e..9c25f35 100644 ---- dat/leap/parm/lipid11.dat -+++ dat/leap/parm/lipid11.dat -@@ -1,4 +1,4 @@ --AMBER Lipid 2011 Force Field (v1.0), A.Skjevik, B. Madej, K.Teigen & R.C.Walker -+** Warning: Lipid11 is deprecated. Please refer to Amber Lipid14 for more information ** AMBER Lipid 2011 Force Field (v1.0), A.Skjevik, B. Madej, K.Teigen & R.C.Walker - cC 12.01 carbonyl sp2 carbon (GAFF c -) - cB 12.01 aliphatic sp2 carbon (GAFF c2-) - cA 12.01 sp3 carbon (GAFF c3-) -diff --git dat/leap/parm/lipid14.dat dat/leap/parm/lipid14.dat -index 46da737..f102976 100644 ---- dat/leap/parm/lipid14.dat -+++ dat/leap/parm/lipid14.dat -@@ -3,59 +3,81 @@ cA 12.01 sp3 carbon (GAFF c3-head,glycerol) - cB 12.01 aliphatic sp2 carbon (GAFF c2-tail) - cC 12.01 carbonyl sp2 carbon (GAFF c -head,glycerol) - cD 12.010 sp3 carbon (GAFFlipid a3-tail) -+hA 1.008 H bonded to aliphatic carbon without electrwd. group (GAFF hc-) -+hB 1.008 H bonded to aromatic carbon (GAFF ha-) -+hE 1.008 H bonded to aliphatic carbon with 1 electrwd. group (GAFF h1-) -+hL 1.008 H bonded to aliphatic carbon without electrwd. group (GAFFlipid hl-) -+hN 1.008 H bonded to nitrogen (GAFF hn-) -+hO 1.008 H in Hydroxyl group (GAFF ho-) -+hX 1.008 H bonded to C next to positively charged group (GAFF hx-) -+nA 14.01 sp3 N with four connected atoms (GAFF n4-) - oC 16.00 sp2 oxygen with one connected atom (e.g C=O, COO-) (GAFF o -) --oS 16.00 sp3 oxygen in ethers and esters (GAFF os-) -+oH 16.00 sp3 oxygen in hydroxyl group (GAFF oh-) - oP 16.00 sp2 oxygen with one connected atom (e.g P-O) in phosphate group (GAFF o -) -+oS 16.00 sp3 oxygen in ethers and esters (GAFF os-) - oT 16.00 sp3 oxygen bonded to carbon in phosphate group (GAFF os-) --nA 14.01 sp3 N with four connected atoms (GAFF n4-) - pA 30.97 phosphorus with four connected atoms, such as O=P(OH)3 (GAFF p5-) --hE 1.008 H bonded to aliphatic carbon with 1 electrwd. group (GAFF h1-) --hX 1.008 H bonded to C next to positively charged group (GAFF hx-) --hB 1.008 H bonded to aromatic carbon (GAFF ha-) --hN 1.008 H bonded to nitrogen (GAFF hn-) --hL 1.008 H bonded to aliphatic carbon without electrwd. group (GAFFlipid hl-) - - cA cB cC cD oC oS oP oT nA pA hE hX hB hN hL - cA-cA 303.1 1.5350 Lipid11 v1.0 (GAFF c3-c3) -+cA-cB 328.3 1.5080 Lipid11 v1.0 (GAFF c3-c2) -+cA-cD 303.1 1.5350 Lipid14 v2.14(GAFF c3-c3) -+cA-hA 337.3 1.0920 Lipid11 v1.0 (GAFF c3-hc) - cA-hE 335.9 1.0930 Lipid11 v1.0 (GAFF c3-h1) - cA-hX 338.7 1.0910 Lipid11 v1.0 (GAFF c3-hx) - cA-nA 293.6 1.4990 Lipid11 v1.0 (GAFF c3-n4) -+cA-oH 314.1 1.4260 Lipid11 v1.0 (GAFF c3-oh) - cA-oS 301.5 1.4390 Lipid11 v1.0 (GAFF c3-os) - cA-oT 301.5 1.4390 Lipid11 v1.0 (GAFF c3-os) - cB-cB 589.7 1.3240 Lipid11 v1.0 (GAFF c2-c2) -+cB-cD 328.3 1.5080 Lipid14 v2.0 (GAFF c2-c3) - cB-hB 344.3 1.0870 Lipid11 v1.0 (GAFF c2-ha) -+cC-cD 328.3 1.5080 Lipid14 v2.0 (GAFF c -c3) - cC-oC 648.0 1.2140 Lipid11 v1.0 (GAFF c -o ) - cC-oS 411.3 1.3430 Lipid11 v1.0 (GAFF c -os) --cD-cB 328.3 1.5080 Lipid14 v2.0 (GAFF c3-c2) --cD-cC 328.3 1.5080 Lipid14 v2.0 (GAFF c3-c ) - cD-cD 303.1 1.5350 Lipid14 v2.0 (GAFF c3-c3) - cD-hL 337.3 1.0920 Lipid14 v2.0 (GAFF c3-hc) - hN-nA 369.0 1.0330 Lipid11 v1.0 (GAFF hn-n4) -+hO-oH 369.6 0.9740 Lipid11 v1.0 (GAFF ho-oh) - oP-pA 487.7 1.4810 Lipid11 v1.0 (GAFF o -p5) - oT-pA 342.5 1.6020 Lipid11 v1.0 (GAFF os-p5) - - cA-cA-cA 63.210 110.630 Lipid11 v1.0 (GAFF c3-c3-c3) -+cA-cA-cB 63.530 111.440 Lipid11 v1.0 (GAFF c3-c3-c2) -+cA-cA-cD 63.210 110.630 Lipid14 v2.14(GAFF c3-c3-c3) -+cA-cA-hA 46.370 110.050 Lipid11 v1.0 (GAFF c3-c3-hc) - cA-cA-hE 46.360 110.070 Lipid11 v1.0 (GAFF c3-c3-h1) - cA-cA-hX 46.020 111.740 Lipid11 v1.0 (GAFF c3-c3-hx) - cA-cA-nA 64.450 114.320 Lipid11 v1.0 (GAFF c3-c3-n4) -+cA-cA-oH 67.720 109.430 Lipid11 v1.0 (GAFF c3-c3-oh) - cA-cA-oS 67.780 108.420 Lipid11 v1.0 (GAFF c3-c3-os) - cA-cA-oT 67.780 108.420 Lipid11 v1.0 (GAFF c3-c3-os) -+cA-cB-cA 62.700 116.520 Lipid11 v1.0 (GAFF c3-c2-c3) -+cA-cB-cB 64.330 123.420 Lipid11 v1.0 (GAFF c3-c2-c2) -+cA-cB-hB 45.660 117.300 Lipid11 v1.0 (GAFF c3-c2-ha) -+cA-cD-cD 63.210 110.630 Lipid14 v2.14(GAFF c3-c3-c3) -+cA-cD-hL 46.370 110.050 Lipid14 v2.14(GAFF c3-c3-hc) - cA-nA-cA 62.840 110.640 Lipid11 v1.0 (GAFF c3-n4-c3) - cA-nA-hN 46.190 110.110 Lipid11 v1.0 (GAFF c3-n4-hn) -+cA-oH-hO 47.090 108.160 Lipid11 v1.0 (GAFF c3-oh-ho) - cA-oS-cC 63.630 115.140 Lipid11 v1.0 (GAFF c3-os-c ) - cA-oT-pA 78.480 118.000 Lipid11 v1.0 (GAFF c3-os-p5) -+cB-cA-hA 47.030 110.490 Lipid11 v1.0 (GAFF c2-c3-hc) -+cB-cB-cD 64.330 123.420 Lipid14 v2.0 (GAFF c2-c2-c3) - cB-cB-hB 50.040 120.940 Lipid11 v1.0 (GAFF c2-c2-ha) -+cB-cD-cD 63.530 111.440 Lipid14 v2.0 (GAFF c2-c3-c3) - cB-cD-hL 47.030 110.490 Lipid14 v2.0 (GAFF c2-c3-hc) -+cC-cD-cD 63.790 110.530 Lipid14 v2.0 (GAFF c -c3-c3) - cC-cD-hL 47.200 109.680 Lipid14 v2.0 (GAFF c -c3-hc) --cD-cB-cB 64.330 123.420 Lipid14 v2.0 (GAFF c3-c2-c2) -+cD-cA-hA 46.370 110.050 Lipid14 v2.14(GAFF c3-c3-hc) - cD-cB-hB 45.660 117.300 Lipid14 v2.0 (GAFF c3-c2-ha) - cD-cC-oC 68.030 123.110 Lipid14 v2.0 (GAFF c3-c -o ) - cD-cC-oS 69.260 111.960 Lipid14 v2.0 (GAFF c3-c -os) --cD-cD-cB 63.530 111.440 Lipid14 v2.0 (GAFF c3-c3-c2) --cD-cD-cC 63.790 110.530 Lipid14 v2.0 (GAFF c3-c3-c ) - cD-cD-cD 63.210 110.630 Lipid14 v2.0 (GAFF c3-c3-c3) - cD-cD-hL 46.370 110.050 Lipid14 v2.0 (GAFF c3-c3-hc) -+hA-cA-hA 39.430 108.350 Lipid11 v1.0 (GAFF hc-c3-hc) - hE-cA-hE 39.180 109.550 Lipid11 v1.0 (GAFF h1-c3-h1) -+hE-cA-oH 50.970 109.880 Lipid11 v1.0 (GAFF ha-c3-oh) - hE-cA-oS 50.840 108.820 Lipid11 v1.0 (GAFF h1-c3-os) - hE-cA-oT 50.840 108.820 Lipid11 v1.0 (GAFF h1-c3-os) - hL-cD-hL 39.430 108.350 Lipid14 v2.0 (GAFF hc-c3-hc) -@@ -67,86 +89,133 @@ oP-pA-oP 46.010 115.800 Lipid11 v1.0 (GAFF o -p5-o ) - oP-pA-oT 44.010 116.090 Lipid11 v1.0 (GAFF o -p5-os) - oT-pA-oT 45.370 101.770 Lipid11 v1.0 (GAFF os-p5-os) - --cA-cA-cA-hE 1 0.1556 0.0 3.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -c3-c3-X ) --cA-cA-cA-oS 1 0.1556 0.0 3.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -c3-c3-X ) --cA-cA-cA-oT 1 0.1556 0.0 3.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -c3-c3-X ) --cA-cA-nA-cA 1 0.1556 0.0 3.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -c3-n4-X ) --cA-cA-nA-hN 1 0.1556 0.0 3.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -c3-n4-X ) --cA-cA-oT-pA 1 0.3833 0.0 3.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -c3-os-X ) --cA-nA-cA-hX 1 0.1556 0.0 3.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -c3-n4-X ) --cA-oS-cC-oS 1 2.700 180.0 2.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -c -os-X ) --cA-oT-pA-oP 1 0.800 0.0 2.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -os-p5-X ) --cA-oT-pA-oP 1 0.800 0.0 2.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -os-p5-X ) --cA-oT-pA-oT 1 0.25 0.0 -3.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF c3-os-p5-os) --cA-oT-pA-oT 1 1.20 0.0 2.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF c3-os-p5-os) --cB-cB-cD-cD 1 0.3464 0.000 1.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit) --cB-cB-cD-cD 1 -0.5577 0.000 2.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit) --cB-cB-cD-cD 1 -0.2920 0.000 3.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit) --cB-cB-cD-cD 1 -0.0943 0.000 4.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit) --cB-cB-cD-cD 1 0.0226 0.000 5.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit) --cB-cD-cD-cD 1 0.0251 180.000 1.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit) --cB-cD-cD-cD 1 0.0054 180.000 2.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit) --cB-cD-cD-cD 1 0.2007 0.000 3.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit) --cB-cD-cD-cD 1 0.2103 0.000 4.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit) --cB-cD-cD-cD 1 0.0811 0.000 5.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit) --cB-cD-cD-hL 1 0.1556 0.0 3.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.0 (GAFF X -c3-c3-X ) --cC-cD-cD-hL 1 0.1556 0.0 3.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.0 (GAFF X -c3-c3-X ) --cC-oS-cA-cA 1 0.383 0.0 -3.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF c3-c3-os-c ) --cC-oS-cA-cA 1 0.80 180.0 1.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF c3-c3-os-c ) --cC-oS-cA-hE 1 0.3833 0.0 3.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -c3-os-X ) --cD-cB-cB-cD 1 0.3073 180.000 1.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit) --cD-cB-cB-cD 1 4.0051 180.000 2.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit) --cD-cB-cB-cD 1 0.1990 0.000 3.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit) --cD-cB-cB-cD 1 0.3242 0.000 4.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit) --cD-cB-cB-cD 1 -0.0415 0.000 5.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit) --cD-cB-cB-hB 1 6.650 180.0 2.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.0 (GAFF X -c2-c2-X ) --cD-cC-oS-cA 1 2.700 180.000 2.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -c -os-X ) --cD-cD-cC-oC 1 -0.9110 180.000 1.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit) --cD-cD-cC-oC 1 0.7382 180.000 2.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit) --cD-cD-cC-oC 1 0.3290 0.000 3.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit) --cD-cD-cC-oC 1 -0.5864 0.000 4.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit) --cD-cD-cC-oC 1 0.1333 0.000 5.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit) --cD-cD-cC-oS 1 -0.1226 180.000 1.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit) --cD-cD-cC-oS 1 -0.2054 180.000 2.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit) --cD-cD-cC-oS 1 0.1802 0.000 3.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit) --cD-cD-cC-oS 1 0.5107 0.000 4.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit) --cD-cD-cC-oS 1 0.1355 0.000 5.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit) --cD-cD-cD-cC 1 0.1556 0.0 3.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF ) --cD-cD-cD-cD 1 0.3112 180.000 1.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit) --cD-cD-cD-cD 1 -0.1233 180.000 2.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit) --cD-cD-cD-cD 1 0.1149 0.000 3.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit) --cD-cD-cD-cD 1 -0.2199 0.000 4.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit) --cD-cD-cD-cD 1 0.2170 0.000 5.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit) --cD-cD-cD-hL 1 0.16 0.0 3.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.0 (GAFF c3-c3-c3-hc) --hB-cB-cB-hB 1 6.650 180.0 2.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -c2-c2-X ) --hE-cA-cA-hE 1 0.1556 0.0 3.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -c3-c3-X ) --hE-cA-cA-nA 1 0.1556 0.0 3.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -c3-c3-X ) --hE-cA-cA-hX 1 0.1556 0.0 3.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -c3-c3-X ) --hE-cA-cA-oS 1 0.00 0.0 -3.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF h1-c3-c3-os) --hE-cA-cA-oS 1 0.25 0.0 1.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF h1-c3-c3-os) --hE-cA-cA-oT 1 0.00 0.0 -3.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF h1-c3-c3-os) --hE-cA-cA-oT 1 0.25 0.0 1.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF h1-c3-c3-os) --hE-cA-oT-pA 1 0.3833 0.0 3.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -c3-os-X ) --hB-cB-cD-cD 1 0.000 0.0 2.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.0 (GAFF X -c3-c2-X ) --hB-cB-cD-hL 1 0.000 0.0 2.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.0 (GAFF X -c3-c2-X ) --hL-cD-cB-cB 1 0.38 180.0 -3.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.0 (GAFF hc-c3-c2-c2) --hL-cD-cB-cB 1 1.15 0.0 1.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.0 (GAFF hc-c3-c2-c2) --hL-cD-cC-oC 1 0.80 0.0 -1.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.0 (GAFF hc-c3-c -o ) --hL-cD-cC-oC 1 0.08 180.0 3.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.0 (GAFF hc-c3-c -o ) --hL-cD-cC-oS 1 0.000 180.0 2.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.0 (GAFF X -c -c3-X ) --hL-cD-cD-hL 1 0.15 0.0 3.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.0 (GAFF hc-c3-c3-hc) --hN-nA-cA-hX 1 0.1556 0.0 3.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -c3-n4-X ) --hX-cA-cA-oT 1 0.1556 0.0 3.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -c3-c3-X ) --nA-cA-cA-oT 1 0.1556 0.0 3.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -c3-c3-X ) --cA-oS-cC-oC 1 2.70 180.0 -2.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF c3-os-c -o ) --cA-oS-cC-oC 1 1.40 180.0 1.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF c3-os-c -o ) --oS-cA-cA-oS 1 0.144 0.0 -3.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF os-c3-c3-os) --oS-cA-cA-oS 1 1.175 0.0 2.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF os-c3-c3-os) --oT-cA-cA-oS 1 0.144 0.0 -3.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF os-c3-c3-os) --oT-cA-cA-oS 1 1.175 0.0 2.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF os-c3-c3-os) -- -+cA-cA-cA-cA 1 0.18 0.0 -3.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF c3-c3-c3-c3) -+cA-cA-cA-cA 1 0.25 180.0 -2.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF c3-c3-c3-c3) -+cA-cA-cA-cA 1 0.20 180.0 1.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF c3-c3-c3-c3) -+cA-cA-cA-cB 1 0.1556 0.0 3.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -c3-c3-X ) -+cA-cA-cA-cD 1 0.3112 180.000 1.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.14(Lipid14 cD-cD-cD-cD) -+cA-cA-cA-cD 1 -0.1233 180.000 2.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.14(Lipid14 cD-cD-cD-cD) -+cA-cA-cA-cD 1 0.1149 0.000 3.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.14(Lipid14 cD-cD-cD-cD) -+cA-cA-cA-cD 1 -0.2199 0.000 4.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.14(Lipid14 cD-cD-cD-cD) -+cA-cA-cA-cD 1 0.2170 0.000 5.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.14(Lipid14 cD-cD-cD-cD) -+cA-cA-cA-hA 1 0.16 0.0 3.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF c3-c3-c3-hc) -+cA-cA-cA-hE 1 0.1556 0.0 3.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -c3-c3-X ) -+cA-cA-cA-oH 1 0.1556 0.0 3.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -c3-c3-X ) -+cA-cA-cA-oS 1 0.1556 0.0 3.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -c3-c3-X ) -+cA-cA-cA-oT 1 0.1556 0.0 3.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -c3-c3-X ) -+cA-cA-cB-cA 1 0.000 0.0 2.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -c3-c2-X ) -+cA-cA-cB-cB 1 0.000 0.0 2.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -c3-c2-X ) -+cA-cA-cB-hB 1 0.000 0.0 2.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -c3-c2-X ) -+cA-cA-cD-cD 1 0.3112 180.000 1.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.14(Lipid14 cD-cD-cD-cD) -+cA-cA-cD-cD 1 -0.1233 180.000 2.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.14(Lipid14 cD-cD-cD-cD) -+cA-cA-cD-cD 1 0.1149 0.000 3.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.14(Lipid14 cD-cD-cD-cD) -+cA-cA-cD-cD 1 -0.2199 0.000 4.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.14(Lipid14 cD-cD-cD-cD) -+cA-cA-cD-cD 1 0.2170 0.000 5.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.14(Lipid14 cD-cD-cD-cD) -+cA-cA-cD-hL 1 0.16 0.0 3.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.14(GAFF c3-c3-c3-hc) -+cA-cA-nA-cA 1 0.1556 0.0 3.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -c3-n4-X ) -+cA-cA-nA-hN 1 0.1556 0.0 3.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -c3-n4-X ) -+cA-cA-oH-hO 1 0.16 0.0 -3.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF c3-c3-oh-ho) -+cA-cA-oH-hO 1 0.25 0.0 1.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF c3-c3-oh-ho) -+cA-cA-oS-cC 1 0.383 0.0 -3.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF c3-c3-os-c ) -+cA-cA-oS-cC 1 0.80 180.0 1.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF c3-c3-os-c ) -+cA-cA-oT-pA 1 0.3833 0.0 3.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -c3-os-X ) -+cA-cB-cA-hA 1 0.000 0.0 2.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -c3-c2-X ) -+cA-cB-cB-cA 1 6.65 180.0 -2.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF c3-c2-c2-c3) -+cA-cB-cB-cA 1 1.90 180.0 1.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF c3-c2-c2-c3) -+cA-cB-cB-hB 1 6.650 180.000 2.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -c2-c2-X ) -+cA-cD-cD-cD 1 0.3112 180.000 1.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.14(Lipid14 cD-cD-cD-cD) -+cA-cD-cD-cD 1 -0.1233 180.000 2.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.14(Lipid14 cD-cD-cD-cD) -+cA-cD-cD-cD 1 0.1149 0.000 3.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.14(Lipid14 cD-cD-cD-cD) -+cA-cD-cD-cD 1 -0.2199 0.000 4.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.14(Lipid14 cD-cD-cD-cD) -+cA-cD-cD-cD 1 0.2170 0.000 5.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.14(Lipid14 cD-cD-cD-cD) -+cA-cD-cD-hL 1 0.16 0.0 3.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.14(GAFF c3-c3-c3-hc) -+cA-nA-cA-hX 1 0.1556 0.0 3.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -c3-n4-X ) -+cA-oS-cC-cD 1 2.700 180.000 2.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -os-c -X ) -+cA-oS-cC-oC 1 2.70 180.0 -2.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF c3-os-c -o ) -+cA-oS-cC-oC 1 1.40 180.0 1.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF c3-os-c -o ) -+cA-oS-cC-oS 1 2.700 180.0 2.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -c -os-X ) -+cA-oT-pA-oP 1 0.800 0.0 2.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -os-p5-X ) -+cA-oT-pA-oT 1 0.25 0.0 -3.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF c3-os-p5-os) -+cA-oT-pA-oT 1 1.20 0.0 2.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF c3-os-p5-os) -+cB-cA-cA-hA 1 0.1556 0.0 3.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -c3-c3-X ) -+cB-cA-cA-hE 1 0.1556 0.0 3.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -c3-c3-X ) -+cB-cA-cA-oH 1 0.1556 0.0 3.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -c3-c3-X ) -+cB-cB-cA-hA 1 0.38 180.0 -3.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF hc-c3-c2-c2) -+cB-cB-cA-hA 1 1.15 0.0 1.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF hc-c3-c2-c2) -+cB-cB-cD-cD 1 0.3464 0.000 1.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit) -+cB-cB-cD-cD 1 -0.5577 0.000 2.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit) -+cB-cB-cD-cD 1 -0.2920 0.000 3.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit) -+cB-cB-cD-cD 1 -0.0943 0.000 4.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit) -+cB-cB-cD-cD 1 0.0226 0.000 5.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit) -+cB-cB-cD-hL 1 0.38 180.0 -3.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.0 (GAFF c2-c2-c3-hc) -+cB-cB-cD-hL 1 1.15 0.0 1.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.0 (GAFF c2-c2-c3-hc) -+cB-cD-cD-cD 1 0.0251 180.000 1.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit) -+cB-cD-cD-cD 1 0.0054 180.000 2.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit) -+cB-cD-cD-cD 1 0.2007 0.000 3.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit) -+cB-cD-cD-cD 1 0.2103 0.000 4.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit) -+cB-cD-cD-cD 1 0.0811 0.000 5.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit) -+cB-cD-cD-hL 1 0.1556 0.0 3.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.0 (GAFF X -c3-c3-X ) -+cC-cD-cD-cD 1 0.1556 0.0 3.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -c3-c3-X ) -+cC-cD-cD-hL 1 0.1556 0.0 3.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.0 (GAFF X -c3-c3-X ) -+cC-oS-cA-hE 1 0.3833 0.0 3.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -c3-os-X ) -+cD-cA-cA-hA 1 0.16 0.0 3.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.14(GAFF c3-c3-c3-hc) -+cD-cB-cB-cD 1 0.3073 180.000 1.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit) -+cD-cB-cB-cD 1 4.0051 180.000 2.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit) -+cD-cB-cB-cD 1 0.1990 0.000 3.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit) -+cD-cB-cB-cD 1 0.3242 0.000 4.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit) -+cD-cB-cB-cD 1 -0.0415 0.000 5.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit) -+cD-cB-cB-hB 1 6.650 180.0 2.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.0 (GAFF X -c2-c2-X ) -+cD-cD-cA-hA 1 0.16 0.0 3.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.14(GAFF c3-c3-c3-hc) -+cD-cD-cB-hB 1 0.000 0.0 2.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.0 (GAFF X -c3-c2-X ) -+cD-cD-cC-oC 1 -0.9110 180.000 1.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit) -+cD-cD-cC-oC 1 0.7382 180.000 2.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit) -+cD-cD-cC-oC 1 0.3290 0.000 3.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit) -+cD-cD-cC-oC 1 -0.5864 0.000 4.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit) -+cD-cD-cC-oC 1 0.1333 0.000 5.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit) -+cD-cD-cC-oS 1 -0.1226 180.000 1.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit) -+cD-cD-cC-oS 1 -0.2054 180.000 2.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit) -+cD-cD-cC-oS 1 0.1802 0.000 3.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit) -+cD-cD-cC-oS 1 0.5107 0.000 4.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit) -+cD-cD-cC-oS 1 0.1355 0.000 5.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit) -+cD-cD-cD-cD 1 0.3112 180.000 1.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit) -+cD-cD-cD-cD 1 -0.1233 180.000 2.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit) -+cD-cD-cD-cD 1 0.1149 0.000 3.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit) -+cD-cD-cD-cD 1 -0.2199 0.000 4.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit) -+cD-cD-cD-cD 1 0.2170 0.000 5.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.10 (paramfit) -+cD-cD-cD-hL 1 0.16 0.0 3.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.0 (GAFF c3-c3-c3-hc) -+hA-cA-cA-hA 1 0.15 0.0 3.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF hc-c3-c3-hc) -+hA-cA-cA-hE 1 0.1556 0.0 3.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -c3-c3-X ) -+hA-cA-cA-oH 1 0.00 0.0 -3.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF hc-c3-c3-oh) -+hA-cA-cA-oH 1 0.25 0.0 1.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF hc-c3-c3-oh) -+hA-cA-cB-hB 1 0.000 0.0 2.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -c3-c2-X ) -+hA-cA-cD-hL 1 0.15 0.0 3.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.14(GAFF hc-c3-c3-hc) -+hB-cB-cB-hB 1 6.650 180.0 2.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -c2-c2-X ) -+hB-cB-cD-hL 1 0.000 0.0 2.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.0 (GAFF X -c3-c2-X ) -+hE-cA-cA-hE 1 0.1556 0.0 3.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -c3-c3-X ) -+hE-cA-cA-hX 1 0.1556 0.0 3.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -c3-c3-X ) -+hE-cA-cA-nA 1 0.1556 0.0 3.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -c3-c3-X ) -+hE-cA-cA-oS 1 0.00 0.0 -3.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF h1-c3-c3-os) -+hE-cA-cA-oS 1 0.25 0.0 1.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF h1-c3-c3-os) -+hE-cA-cA-oT 1 0.00 0.0 -3.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF h1-c3-c3-os) -+hE-cA-cA-oT 1 0.25 0.0 1.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF h1-c3-c3-os) -+hE-cA-oH-hO 1 0.500 0.0 3.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -c3-oh-X ) -+hE-cA-oT-pA 1 0.3833 0.0 3.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -c3-os-X ) -+hL-cD-cC-oC 1 0.08 180.0 -3.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.0 (GAFF hc-c3-c -o ) -+hL-cD-cC-oC 1 0.80 0.0 1.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.0 (GAFF hc-c3-c -o ) -+hL-cD-cC-oS 1 0.000 180.0 2.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.0 (GAFF X -c -c3-X ) -+hL-cD-cD-hL 1 0.15 0.0 3.000 SCEE=1.2 SCNB=2.0 Lipid14 v2.0 (GAFF hc-c3-c3-hc) -+hN-nA-cA-hX 1 0.1556 0.0 3.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -c3-n4-X ) -+hX-cA-cA-oT 1 0.1556 0.0 3.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -c3-c3-X ) -+nA-cA-cA-oT 1 0.1556 0.0 3.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF X -c3-c3-X ) -+oS-cA-cA-oS 1 0.144 0.0 -3.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF os-c3-c3-os) -+oS-cA-cA-oS 1 1.175 0.0 2.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF os-c3-c3-os) -+oS-cA-cA-oT 1 0.144 0.0 -3.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF os-c3-c3-os) -+oS-cA-cA-oT 1 1.175 0.0 2.000 SCEE=1.2 SCNB=2.0 Lipid11 v1.0 (GAFF os-c3-c3-os) -+ -+cA-cB-cB-cA 1.1 180. 2.0 Lipid14 CHL (GAFF) -+cB-cA-cB-hB 1.1 180. 2.0 Lipid14 CHL (GAFF) -+cB-cD-cB-hB 1.1 180.0 2.0 Lipid14 v2.0 aliphatic improper (GAFF c2-c3-c2-ha) - cD-oC-cC-oS 10.5 180.0 2.0 Lipid14 v2.0 ester improper (GAFF X -X -c -o ) --cB-cD-cB-hB 1.1 180.0 2.0 Lipid14 v2.0 aliphatic improper (GAFF c2-c3-c2-ha - default) - - hw ow 0000. 0000. 4. flag for fast water - Hack for no 10-12 terms - -@@ -156,17 +225,20 @@ MOD4 RE - cB 1.9080 0.0860 Lipid14 v2.10 - cC 1.9080 0.0700 Lipid14 v2.10 - cD 1.9080 0.1094 OPLS -+ hA 1.4870 0.0157 OPLS -+ hB 1.2500 0.0070 Lipid14 v2.10 -+ hE 1.3870 0.0157 Veenstra et al JCC,8,(1992),963 -+ hL 1.4600 0.0100 Lipid14 v2.10 -+ hN 0.6000 0.0157 !Ferguson base pair geom. -+ hO 0.0000 0.0000 OPLS Jorgensen, JACS,110,(1988),1657 (RCW Needs fixing give radii) -+ hX 1.1000 0.0157 Veenstra et al JCC,8,(1992),963 -+ nA 1.8240 0.1700 OPLS - oC 1.6500 0.1400 Lipid14 v2.10 -+ oH 1.7210 0.2104 OPLS -+ oP 1.6500 0.1400 Lipid14 v2.10 - oS 1.6500 0.1200 Lipid14 v2.10 - oT 1.6500 0.1200 Lipid14 v2.10 -- oP 1.6500 0.1400 Lipid14 v2.10 -- nA 1.8240 0.1700 OPLS - pA 2.1000 0.2000 JCC,7,(1986),230; -- hE 1.3870 0.0157 Veenstra et al JCC,8,(1992),963 -- hX 1.1000 0.0157 Veenstra et al JCC,8,(1992),963 -- hB 1.2500 0.0070 Lipid14 v2.10 -- hN 0.6000 0.0157 !Ferguson base pair geom. -- hL 1.4600 0.0100 Lipid14 v2.10 - - END - -@@ -175,7 +247,7 @@ END - - *** AMBER Lipid14 Force Field, C. Dickson, B. Madej, A.Skjevik, K. Teigen, I.R. Gould, R.C. Walker *** - --Citation is - Released version 2.10: -+Citation is: - - Dickson, C.J., Madej, B.D., Skjevik, A.A., Betz, R.M., Teigen, K., Gould, I.R., Walker, R.C., "Lipid14: The Amber Lipid Force Field", J. Chem. Theory Comput., 2014, in press, DOI: 10.1021/ct4010307 - -@@ -241,24 +313,31 @@ Version 2.11 (February 2014) - Version 2.12 (February 2014) - - Replace angle force constants involving phosporus with the correct values from the update GAFF.dat file. - -+Version 2.14 (September 2015) -+- Reorder parameters so they are alphabetical. -+- Add cholesterol parameters -+ - Atom type mapping - ----------------- - - GAFF Lipid14 Description - ---- ------- ----------- -- c3 cA sp3 carbon -- c2 cB aliphatic sp2 carbon - c cC carbonyl sp2 carbon -- o oC sp2 oxygen with one connected atom (e.g C=O, COO-) -- os oS sp3 oxygen in ethers and esters -- n4 nA sp3 N with four connected atoms -- p5 pA phosphorus with four connected atoms, such as O=P(OH)3 -+ c2 cB aliphatic sp2 carbon -+ c3 cA sp3 carbon - h1 hE H bonded to aliphatic carbon with 1 electrwd. group -- hx hX H bonded to C next to positively charged group - ha hB H bonded to aromatic carbon -+ hc hA H bonded to aliphatic carbon without electrwd. group - hn hN H bonded to nitrogen -+ ho hO H in Hydroxyl group -+ hx hX H bonded to C next to positively charged group -+ n4 nA sp3 N with four connected atoms -+ o oC sp2 oxygen with one connected atom (e.g C=O, COO-) - o oP sp2 oxygen with one connected atom (e.g P-O) in phosphate group -+ oh oH sp3 oxygen in hydroxyl group -+ os oS sp3 oxygen in ethers and esters - os oT sp3 oxygen bonded to carbon in phosphate group -+ p5 pA phosphorus with four connected atoms, such as O=P(OH)3 - - GAFFlipid Lipid14 Description - --------- ------- ----------- |