diff options
| author |   Reinis Danne <rei4dan@gmail.com> | 2016-01-20 23:00:58 +0200 |
|---|---|---|
| committer | Reinis Danne <rei4dan@gmail.com> | 2016-01-20 23:00:58 +0200 |
| commit | a471a9cb405d6445c994bc5852fb11c930d7ac9f (patch) | |
| tree | 04679d6d5fc7484cda6b8352e0255b469d5f5487 /sci-chemistry/ambertools/files/ambertools-15-update.4.patch | |
| parent | Merge pull request #569 from TheChymera/psychopy (diff) | |
| download | sci-ambertools.tar.gz sci-ambertools.tar.bz2 sci-ambertools.zip | |
sci-chemistry/ambertools: Version bump to 15ambertools
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, 908 insertions, 0 deletions
diff --git a/sci-chemistry/ambertools/files/ambertools-15-update.4.patch b/sci-chemistry/ambertools/files/ambertools-15-update.4.patch new file mode 100644 index 000000000..4176a583a --- /dev/null +++ b/sci-chemistry/ambertools/files/ambertools-15-update.4.patch @@ -0,0 +1,908 @@ +*******> 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 + --------- ------- ----------- |