├── .gitignore ├── 15leu2x ├── Instructions.pdf └── input │ ├── 15leu2x.psf │ ├── 15leu2x.s0.equil.coor │ ├── 15leu2x.s0.pdb │ ├── 15leu2x.s1.equil.coor │ ├── 15leu2x.s1.pdb │ ├── 15leu2x.s2.equil.coor │ ├── 15leu2x.s2.pdb │ ├── 15leu2x.s3.equil.coor │ ├── 15leu2x.s3.pdb │ ├── 15leu2x.s4.equil.coor │ ├── 15leu2x.s4.pdb │ ├── 15leu2x.s5.equil.coor │ ├── 15leu2x.s5.pdb │ ├── 15leu2x.s6.equil.coor │ ├── 15leu2x.s6.pdb │ ├── 15leu2x.s7.equil.coor │ ├── 15leu2x.s7.pdb │ ├── 15leu2x.s8.equil.coor │ ├── 15leu2x.s8.pdb │ ├── 15leu2x.s9.equil.coor │ ├── 15leu2x.s9.pdb │ ├── README.txt │ ├── abf.namd │ ├── alpha_ideal_ref.xyz │ ├── calc_variables.tcl │ ├── clear_pbc.tcl │ ├── colvar_display.tcl │ ├── demo.tcl │ ├── demo.vmd │ ├── dist_orient.colvars.in │ ├── drag_1d.namd │ ├── drag_6d.namd │ ├── force_helical_structure.colvars.in │ ├── mtd_1d.namd │ ├── mtd_2d.namd │ ├── packing_angles.colvars.in │ ├── par_all36_prot.prm │ ├── plot_colvars_traj.py │ ├── quaternion2rmatrix.tcl │ ├── restrain_helixA.colvars.in │ ├── show_rotation_axis.tcl │ ├── show_variables.tcl │ └── unbind.namd ├── README.md ├── symmetric_DBC ├── AFEP.colvars ├── README.md ├── RFEP_vacuum.colvars ├── ref.pdb └── ref_vacuum.pdb └── tma-aco ├── Common ├── charmm │ ├── par_all22_prot.prm │ ├── par_all35_ethers.prm │ ├── par_all36_carb.prm │ ├── par_all36_cgenff.prm │ ├── par_all36_lipid.prm │ ├── par_all36_na.prm │ ├── par_all36_prot.prm │ ├── par_all36m_prot.prm │ ├── top_all22_prot.rtf │ ├── top_all35_ethers.rtf │ ├── top_all36_carb.rtf │ ├── top_all36_cgenff.rtf │ ├── top_all36_lipid.rtf │ ├── top_all36_na.rtf │ ├── top_all36_prot.rtf │ └── toppar_water_ions.str ├── common.namd ├── distance.colvars.in ├── tma-aco.ndx ├── tma-aco.pdb ├── tma-aco.psf ├── tma-aco.xsc └── write_index_file.tcl ├── README.md ├── abf └── abf.namd ├── mtd-ti └── mtd-ti.namd ├── mtd └── mtd.namd ├── smd-ti └── smd-ti.namd ├── smd └── smd.namd ├── test └── test.namd ├── us-ti └── us-ti.namd └── us └── us.namd /.gitignore: -------------------------------------------------------------------------------- 1 | *~ 2 | *.o 3 | *.so 4 | *.a 5 | *.x 6 | *.exe 7 | *.pyc 8 | 9 | .*.swp 10 | 11 | # output files from NAMD 12 | *.diff 13 | *.BAK 14 | *.old 15 | *.coor 16 | *.coor.dcd 17 | *.vel 18 | *.xsc 19 | *.backup 20 | *.state 21 | *.traj 22 | *.out 23 | *.err 24 | *.count 25 | *.grad 26 | *.pmf 27 | # output files from file-based mw-metadynamics 28 | *.rep?.files.txt 29 | replicas.registry.txt 30 | *.rep?.hills 31 | -------------------------------------------------------------------------------- /15leu2x/Instructions.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Colvars/examples/a5f8c707e13f68736fc7372e2d42329364088ead/15leu2x/Instructions.pdf -------------------------------------------------------------------------------- /15leu2x/input/15leu2x.s0.equil.coor: 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-------------------------------------------------------------------------------- https://raw.githubusercontent.com/Colvars/examples/a5f8c707e13f68736fc7372e2d42329364088ead/15leu2x/input/15leu2x.s9.equil.coor -------------------------------------------------------------------------------- /15leu2x/input/README.txt: -------------------------------------------------------------------------------- 1 | Here are the links to download individual DCD files for the existing trajectories from: 2 | 3 | https://github.com/Colvars/datasets/blob/master/15leu2x/trajectories/15leu2x.s0.equil.dcd?raw=true 4 | https://github.com/Colvars/datasets/blob/master/15leu2x/trajectories/15leu2x.s1.equil.dcd?raw=true 5 | https://github.com/Colvars/datasets/blob/master/15leu2x/trajectories/15leu2x.s2.equil.dcd?raw=true 6 | https://github.com/Colvars/datasets/blob/master/15leu2x/trajectories/15leu2x.s3.equil.dcd?raw=true 7 | https://github.com/Colvars/datasets/blob/master/15leu2x/trajectories/15leu2x.s4.equil.dcd?raw=true 8 | https://github.com/Colvars/datasets/blob/master/15leu2x/trajectories/15leu2x.s5.equil.dcd?raw=true 9 | https://github.com/Colvars/datasets/blob/master/15leu2x/trajectories/15leu2x.s6.equil.dcd?raw=true 10 | https://github.com/Colvars/datasets/blob/master/15leu2x/trajectories/15leu2x.s7.equil.dcd?raw=true 11 | https://github.com/Colvars/datasets/blob/master/15leu2x/trajectories/15leu2x.s8.equil.dcd?raw=true 12 | https://github.com/Colvars/datasets/blob/master/15leu2x/trajectories/15leu2x.s9.equil.dcd?raw=true 13 | 14 | 15 | Entire repository: 16 | 17 | https://github.com/Colvars/datasets/archive/master.zip 18 | -------------------------------------------------------------------------------- /15leu2x/input/abf.namd: -------------------------------------------------------------------------------- 1 | # -*- tcl -*- 2 | 3 | # ABF protocol 4 | 5 | cv config " 6 | 7 | # This string is not Tcl code, but you can still use in here Tcl variables, 8 | # such as ${numsteps}, and bracket expansion, such as [outputEnergies]. 9 | 10 | abf { 11 | 12 | name m 13 | 14 | colvars r 15 | 16 | # ABF may try too hard to integrate highly repulsive barriers: this option 17 | # is an attempt at preventing that 18 | maxForce 50.0 19 | }" 20 | -------------------------------------------------------------------------------- /15leu2x/input/alpha_ideal_ref.xyz: -------------------------------------------------------------------------------- 1 | 15 2 | generated by VMD 3 | CA 2.213254 0.495112 9.106215 4 | CA 0.279932 -2.374736 7.438818 5 | CA -2.218335 0.126387 5.931921 6 | CA 0.627902 2.302538 4.545001 7 | CA 2.400020 -0.788910 3.106003 8 | CA -0.866146 -1.993106 1.473764 9 | CA -1.511858 1.503829 0.014659 10 | CA 2.080043 1.724728 -1.346521 11 | CA 1.829868 -1.789091 -2.886153 12 | CA -1.584722 -0.939080 -4.420992 13 | CA -0.256507 2.362945 -5.865771 14 | CA 2.755691 0.532462 -7.388165 15 | CA 0.459064 -2.199475 -8.827452 16 | CA -1.949627 0.430335 -10.265867 17 | CA 0.963421 2.383063 -11.836460 18 | -------------------------------------------------------------------------------- /15leu2x/input/calc_variables.tcl: -------------------------------------------------------------------------------- 1 | 2 | puts -nonewline [cv printframelabels] 3 | for { set frame 0 } { ${frame} < [molinfo top get numframes] } { incr frame } { 4 | cv frame ${frame} 5 | cv update 6 | puts -nonewline [cv printframe] 7 | } 8 | -------------------------------------------------------------------------------- /15leu2x/input/clear_pbc.tcl: -------------------------------------------------------------------------------- 1 | # When a DCD file was written without PBC information, VMD usually adds a PBC 2 | # cubic unit cell with 1 Angstrom edge. 3 | # 4 | # Run this script from inside VMD to set the PBC vectors to zero (as they should) with: 5 | # source clear_pbc.tcl 6 | 7 | for { set frame 0 } { ${frame} < [molinfo top get numframes] } { incr frame } { 8 | animate goto ${frame} 9 | molinfo top set { "a" "b" "c" } { 0.0 0.0 0.0 } 10 | } 11 | -------------------------------------------------------------------------------- /15leu2x/input/colvar_display.tcl: -------------------------------------------------------------------------------- 1 | # Real-time display of colvar values in a VMD scene 2 | # 3 | # Example usage: 4 | # 5 | # cv molid top 6 | # cv configfile my_colvars.in 7 | # 8 | # start_colvar_display "cv1 cv2" yellow # text color 9 | # set_colvar_display position { 0 0 5 } # change text position 10 | # stop_colvar_display 11 | # 12 | # start_rotation_display orientation 13 | # stop_rotation_display 14 | # 15 | ########################################################### 16 | 17 | proc start_colvar_display { {cvs all} {text_color blue} {text_position {15 15 15}} {molid top} } { 18 | 19 | global text_pos text_col cv_handle cv_list vmd_frame 20 | 21 | set text_pos $text_position 22 | set text_col $text_color 23 | set cv_handle -1 24 | set cv_list $cvs 25 | 26 | if {! [string compare $molid top]} { 27 | set molid [molinfo top] 28 | } 29 | 30 | # draw values right away 31 | update_colvar_display vmd_frame $molid w 32 | 33 | # set trace 34 | global vmd_frame 35 | trace add variable vmd_frame($molid) write update_colvar_display 36 | return 37 | } 38 | 39 | 40 | ########################################################### 41 | proc stop_colvar_display { {molid top} } { 42 | global cv_handle vmd_frame 43 | 44 | if { $cv_handle > -1 } { 45 | graphics $molid delete $cv_handle 46 | } 47 | if {! [string compare $molid top]} { 48 | set molid [molinfo top] 49 | } 50 | trace remove variable vmd_frame($molid) write update_colvar_display 51 | return 52 | } 53 | 54 | ########################################################### 55 | proc set_colvar_display { property value } { 56 | global text_pos text_col 57 | 58 | switch $property { 59 | "color" { set text_col $value } 60 | "position" { set text_pos $value } 61 | default { puts "Possible properties: color, position" } 62 | } 63 | 64 | update_colvar_display vmd_frame [molinfo top] w 65 | return 66 | } 67 | 68 | 69 | ########################################################### 70 | proc update_colvar_display {name molid op} { 71 | # name == vmd_frame 72 | # molid == molecule id of the newly changed frame 73 | # op == w 74 | 75 | global text_pos text_col cv_handle cv_list 76 | set f [molinfo $molid get frame] 77 | cv frame $f 78 | 79 | if {! [string compare $cv_list all]} { 80 | set cv [cv list] 81 | } else { 82 | set cv $cv_list 83 | } 84 | 85 | if { $cv_handle > -1 } { 86 | graphics $molid replace $cv_handle 87 | } 88 | 89 | foreach v $cv { 90 | # Calculate only requested variables 91 | set value [cv colvar $v update] 92 | # Parse vectors 93 | set value [regsub -all {,|\(|\)} $value ""] 94 | append t [format "%s=" $v] 95 | foreach x $value { append t [format "%8.2f " $x] } 96 | } 97 | 98 | graphics $molid color $text_col 99 | set cv_handle [graphics $molid text $text_pos $t] 100 | return 101 | } 102 | 103 | ########################################################### 104 | ########################################################### 105 | # Display rotations as axis + "clock hands" 106 | ########################################################### 107 | ########################################################### 108 | proc start_rotation_display { cv {color yellow} {position {0 0 0}} {molid top} } { 109 | 110 | global rot_pos rot_col rot_handle rot_cv vmd_frame 111 | 112 | set rot_pos $position 113 | set rot_col $color 114 | set rot_handle "" 115 | set rot_cv $cv 116 | 117 | if {! [string compare $molid top]} { 118 | set molid [molinfo top] 119 | } 120 | 121 | # draw values right away 122 | update_rotation_display vmd_frame $molid w 123 | 124 | # set trace 125 | global vmd_frame 126 | trace add variable vmd_frame($molid) write update_rotation_display 127 | return 128 | } 129 | 130 | ########################################################### 131 | proc stop_rotation_display { {molid top} } { 132 | global rot_handle vmd_frame 133 | 134 | foreach h $rot_handle { 135 | graphics $molid delete $h 136 | } 137 | if {! [string compare $molid top]} { 138 | set molid [molinfo top] 139 | } 140 | trace remove variable vmd_frame($molid) write update_rotation_display 141 | return 142 | } 143 | 144 | ########################################################### 145 | proc set_rotation_display { property value } { 146 | global rot_pos rot_col 147 | 148 | switch $property { 149 | "color" { set rot_col $value } 150 | "position" { set rot_pos $value } 151 | default { puts "Possible properties: color, position" } 152 | } 153 | 154 | update_rotation_display vmd_frame [molinfo top] w 155 | return 156 | } 157 | 158 | 159 | ########################################################### 160 | proc update_rotation_display {name molid op} { 161 | # name == vmd_frame 162 | # molid == molecule id of the newly changed frame 163 | # op == w 164 | 165 | # Geometric parameters: lengths and radii of cylinders 166 | set L 12. ;# length of main axis 167 | set R 0.7 ;# radius of main axis 168 | set l 5. ;# length of "clock handles" 169 | set r 0.5 ;# radius of "clock handles" 170 | set tip_ratio 4. ;# cone length divided by main radius 171 | set res 16 ;# resolution of all objects 172 | ###################################################### 173 | 174 | 175 | global rot_pos rot_col rot_handle rot_cv M_PI 176 | set f [molinfo $molid get frame] 177 | cv frame $f 178 | 179 | foreach h $rot_handle { 180 | graphics $molid delete $h 181 | } 182 | 183 | set value [cv colvar $rot_cv update] 184 | # Parse vector 185 | set value [regsub -all {,|\(|\)} $value ""] 186 | foreach {q0 q1 q2 q3} $value {} 187 | 188 | graphics $molid color $rot_col 189 | 190 | set theta [expr {2.0 * 180. / $M_PI * acos($q0)}] 191 | if {$theta*$theta < 1e-12} { 192 | lappend rot_handle [graphics $molid sphere $rot_pos radius $R resolution $res] 193 | } else { 194 | 195 | set factor [expr {$L / sqrt(1-$q0*$q0) / 2.}] 196 | # u has the half-length of the main cylinder 197 | set u [vecscale $factor "$q1 $q2 $q3"] 198 | if { $q1 == 0. } { 199 | set v1 [vecnorm [veccross $u "0. 1. 0."]] 200 | } else { 201 | set v1 [vecnorm [veccross $u "1. 0. 0."]] 202 | } 203 | set v2 [vectrans [transabout $u $theta] $v1] 204 | 205 | set e1 [vecadd $rot_pos [vecscale $l $v1]] 206 | set e2 [vecadd $rot_pos [vecscale $l $v2]] 207 | lappend rot_handle [graphics $molid cylinder [vecsub $rot_pos $u] [vecadd $rot_pos $u] radius $R resolution $res filled yes] 208 | set tip [vecadd [vecadd $rot_pos $u] [vecscale $u [expr {2. * $tip_ratio * $R / $L}]]] 209 | lappend rot_handle [graphics $molid cone [vecadd $rot_pos $u] $tip radius [expr {1.5 * $R}] resolution $res] 210 | lappend rot_handle [graphics $molid cylinder $rot_pos $e1 radius $r resolution $res filled yes] 211 | lappend rot_handle [graphics $molid cylinder $rot_pos $e2 radius $r resolution $res filled yes] 212 | } 213 | 214 | return 215 | } 216 | 217 | -------------------------------------------------------------------------------- /15leu2x/input/demo.tcl: -------------------------------------------------------------------------------- 1 | 2 | cv molid top 3 | cv configfile dist_orient.colvars.in 4 | 5 | play colvar_display.tcl 6 | start_colvar_display orient -------------------------------------------------------------------------------- /15leu2x/input/demo.vmd: -------------------------------------------------------------------------------- 1 | #!/usr/local/bin/vmd 2 | # VMD script written by save_state $Revision: 1.47 $ 3 | # VMD version: 1.9.2 4 | set viewplist {} 5 | set fixedlist {} 6 | proc vmdrestoremymaterials {} { 7 | set mlist { Opaque Transparent BrushedMetal Diffuse Ghost Glass1 Glass2 Glass3 Glossy HardPlastic MetallicPastel Steel Translucent Edgy EdgyShiny EdgyGlass Goodsell AOShiny AOChalky AOEdgy BlownGlass GlassBubble RTChrome } 8 | set mymlist [material list] 9 | foreach mat $mlist { 10 | if { [lsearch $mymlist $mat] == -1 } { 11 | material add $mat 12 | } 13 | } 14 | material change ambient Opaque 0.000000 15 | material change diffuse Opaque 0.650000 16 | material change specular Opaque 0.500000 17 | material change shininess Opaque 0.534020 18 | material change mirror Opaque 0.000000 19 | material change opacity Opaque 1.000000 20 | material change outline Opaque 0.000000 21 | material change outlinewidth Opaque 0.000000 22 | material change transmode Opaque 0.000000 23 | material change ambient Transparent 0.000000 24 | material change diffuse Transparent 0.650000 25 | material change specular Transparent 0.500000 26 | material change shininess Transparent 0.534020 27 | material change mirror Transparent 0.000000 28 | material change opacity Transparent 0.300000 29 | material change outline Transparent 0.000000 30 | material change outlinewidth Transparent 0.000000 31 | material change transmode Transparent 0.000000 32 | material change ambient BrushedMetal 0.080000 33 | material change diffuse BrushedMetal 0.390000 34 | material change specular BrushedMetal 0.340000 35 | material change shininess BrushedMetal 0.150000 36 | material change mirror BrushedMetal 0.000000 37 | material change opacity BrushedMetal 1.000000 38 | material change outline BrushedMetal 0.000000 39 | material change outlinewidth BrushedMetal 0.000000 40 | material change transmode BrushedMetal 0.000000 41 | material change ambient Diffuse 0.000000 42 | material change diffuse Diffuse 0.620000 43 | material change specular Diffuse 0.000000 44 | material change shininess Diffuse 0.530000 45 | material change mirror Diffuse 0.000000 46 | material change opacity Diffuse 1.000000 47 | material change outline Diffuse 0.000000 48 | material change outlinewidth Diffuse 0.000000 49 | material change transmode Diffuse 0.000000 50 | material change ambient Ghost 0.000000 51 | material change diffuse Ghost 0.000000 52 | material change specular Ghost 1.000000 53 | material change shininess Ghost 0.230000 54 | material change mirror Ghost 0.000000 55 | material change opacity Ghost 0.100000 56 | material change outline Ghost 0.000000 57 | material change outlinewidth Ghost 0.000000 58 | material change transmode Ghost 0.000000 59 | material change ambient Glass1 0.000000 60 | material change diffuse Glass1 0.500000 61 | material change specular Glass1 0.650000 62 | material change shininess Glass1 0.530000 63 | material change mirror Glass1 0.000000 64 | material change opacity Glass1 0.150000 65 | material change outline Glass1 0.000000 66 | material change outlinewidth Glass1 0.000000 67 | material change transmode Glass1 0.000000 68 | material change ambient Glass2 0.520000 69 | material change diffuse Glass2 0.760000 70 | material change specular Glass2 0.220000 71 | material change shininess Glass2 0.590000 72 | material change mirror Glass2 0.000000 73 | material change opacity Glass2 0.680000 74 | material change outline Glass2 0.000000 75 | material change outlinewidth Glass2 0.000000 76 | material change transmode Glass2 0.000000 77 | material change ambient Glass3 0.150000 78 | material change diffuse Glass3 0.250000 79 | material change specular Glass3 0.750000 80 | material change shininess Glass3 0.800000 81 | material change mirror Glass3 0.000000 82 | material change opacity Glass3 0.500000 83 | material change outline Glass3 0.000000 84 | material change outlinewidth Glass3 0.000000 85 | material change transmode Glass3 0.000000 86 | material change ambient Glossy 0.000000 87 | material change diffuse Glossy 0.650000 88 | material change specular Glossy 1.000000 89 | material change shininess Glossy 0.880000 90 | material change mirror Glossy 0.000000 91 | material change opacity Glossy 1.000000 92 | material change outline Glossy 0.000000 93 | material change outlinewidth Glossy 0.000000 94 | material change transmode Glossy 0.000000 95 | material change ambient HardPlastic 0.000000 96 | material change diffuse HardPlastic 0.560000 97 | material change specular HardPlastic 0.280000 98 | material change shininess HardPlastic 0.690000 99 | material change mirror HardPlastic 0.000000 100 | material change opacity HardPlastic 1.000000 101 | material change outline HardPlastic 0.000000 102 | material change outlinewidth HardPlastic 0.000000 103 | material change transmode HardPlastic 0.000000 104 | material change ambient MetallicPastel 0.000000 105 | material change diffuse MetallicPastel 0.260000 106 | material change specular MetallicPastel 0.550000 107 | material change shininess MetallicPastel 0.190000 108 | material change mirror MetallicPastel 0.000000 109 | material change opacity MetallicPastel 1.000000 110 | material change outline MetallicPastel 0.000000 111 | material change outlinewidth MetallicPastel 0.000000 112 | material change transmode MetallicPastel 0.000000 113 | material change ambient Steel 0.250000 114 | material change diffuse Steel 0.000000 115 | material change specular Steel 0.380000 116 | material change shininess Steel 0.320000 117 | material change mirror Steel 0.000000 118 | material change opacity Steel 1.000000 119 | material change outline Steel 0.000000 120 | material change outlinewidth Steel 0.000000 121 | material change transmode Steel 0.000000 122 | material change ambient Translucent 0.000000 123 | material change diffuse Translucent 0.700000 124 | material change specular Translucent 0.600000 125 | material change shininess Translucent 0.300000 126 | material change mirror Translucent 0.000000 127 | material change opacity Translucent 0.800000 128 | material change outline Translucent 0.000000 129 | material change outlinewidth Translucent 0.000000 130 | material change transmode Translucent 0.000000 131 | material change ambient Edgy 0.000000 132 | material change diffuse Edgy 0.660000 133 | material change specular Edgy 0.000000 134 | material change shininess Edgy 0.750000 135 | material change mirror Edgy 0.000000 136 | material change opacity Edgy 1.000000 137 | material change outline Edgy 0.620000 138 | material change outlinewidth Edgy 0.940000 139 | material change transmode Edgy 0.000000 140 | material change ambient EdgyShiny 0.000000 141 | material change diffuse EdgyShiny 0.660000 142 | material change specular EdgyShiny 0.960000 143 | material change shininess EdgyShiny 0.750000 144 | material change mirror EdgyShiny 0.000000 145 | material change opacity EdgyShiny 1.000000 146 | material change outline EdgyShiny 0.760000 147 | material change outlinewidth EdgyShiny 0.940000 148 | material change transmode EdgyShiny 0.000000 149 | material change ambient EdgyGlass 0.000000 150 | material change diffuse EdgyGlass 0.660000 151 | material change specular EdgyGlass 0.500000 152 | material change shininess EdgyGlass 0.750000 153 | material change mirror EdgyGlass 0.000000 154 | material change opacity EdgyGlass 0.620000 155 | material change outline EdgyGlass 0.620000 156 | material change outlinewidth EdgyGlass 0.940000 157 | material change transmode EdgyGlass 0.000000 158 | material change ambient Goodsell 0.520000 159 | material change diffuse Goodsell 1.000000 160 | material change specular Goodsell 0.000000 161 | material change shininess Goodsell 0.000000 162 | material change mirror Goodsell 0.000000 163 | material change opacity Goodsell 1.000000 164 | material change outline Goodsell 4.000000 165 | material change outlinewidth Goodsell 0.900000 166 | material change transmode Goodsell 0.000000 167 | material change ambient AOShiny 0.000000 168 | material change diffuse AOShiny 0.850000 169 | material change specular AOShiny 0.200000 170 | material change shininess AOShiny 0.530000 171 | material change mirror AOShiny 0.000000 172 | material change opacity AOShiny 1.000000 173 | material change outline AOShiny 0.000000 174 | material change outlinewidth AOShiny 0.000000 175 | material change transmode AOShiny 0.000000 176 | material change ambient AOChalky 0.000000 177 | material change diffuse AOChalky 0.850000 178 | material change specular AOChalky 0.000000 179 | material change shininess AOChalky 0.530000 180 | material change mirror AOChalky 0.000000 181 | material change opacity AOChalky 1.000000 182 | material change outline AOChalky 0.000000 183 | material change outlinewidth AOChalky 0.000000 184 | material change transmode AOChalky 0.000000 185 | material change ambient AOEdgy 0.000000 186 | material change diffuse AOEdgy 0.900000 187 | material change specular AOEdgy 0.200000 188 | material change shininess AOEdgy 0.530000 189 | material change mirror AOEdgy 0.000000 190 | material change opacity AOEdgy 1.000000 191 | material change outline AOEdgy 0.620000 192 | material change outlinewidth AOEdgy 0.930000 193 | material change transmode AOEdgy 0.000000 194 | material change ambient BlownGlass 0.040000 195 | material change diffuse BlownGlass 0.340000 196 | material change specular BlownGlass 1.000000 197 | material change shininess BlownGlass 1.000000 198 | material change mirror BlownGlass 0.000000 199 | material change opacity BlownGlass 0.100000 200 | material change outline BlownGlass 0.000000 201 | material change outlinewidth BlownGlass 0.000000 202 | material change transmode BlownGlass 1.000000 203 | material change ambient GlassBubble 0.250000 204 | material change diffuse GlassBubble 0.340000 205 | material change specular GlassBubble 1.000000 206 | material change shininess GlassBubble 1.000000 207 | material change mirror GlassBubble 0.000000 208 | material change opacity GlassBubble 0.040000 209 | material change outline GlassBubble 0.000000 210 | material change outlinewidth GlassBubble 0.000000 211 | material change transmode GlassBubble 1.000000 212 | material change ambient RTChrome 0.000000 213 | material change diffuse RTChrome 0.650000 214 | material change specular RTChrome 0.500000 215 | material change shininess RTChrome 0.530000 216 | material change mirror RTChrome 0.700000 217 | material change opacity RTChrome 1.000000 218 | material change outline RTChrome 0.000000 219 | material change outlinewidth RTChrome 0.000000 220 | material change transmode RTChrome 0.000000 221 | } 222 | vmdrestoremymaterials 223 | # Atom selection macros 224 | atomselect macro at {resname ADE A THY T 225 | } 226 | atomselect macro acidic {resname ASP GLU 227 | } 228 | atomselect macro cyclic {resname HIS PHE PRO TRP TYR 229 | } 230 | atomselect macro acyclic {protein and not cyclic 231 | } 232 | atomselect macro aliphatic {resname ALA GLY ILE LEU VAL 233 | } 234 | atomselect macro alpha {protein and name CA 235 | } 236 | atomselect macro amino {protein 237 | } 238 | atomselect macro aromatic {resname HIS PHE TRP TYR 239 | } 240 | atomselect macro basic {resname ARG HIS LYS HSP 241 | } 242 | atomselect macro bonded {numbonds > 0 243 | } 244 | atomselect macro buried {resname ALA LEU VAL ILE PHE CYS MET TRP 245 | } 246 | atomselect macro cg {resname CYT C GUA G 247 | } 248 | atomselect macro charged {basic or acidic 249 | } 250 | atomselect macro hetero {not (protein or nucleic) 251 | } 252 | atomselect macro hydrophobic {resname ALA LEU VAL ILE PRO PHE MET TRP 253 | } 254 | atomselect macro small {resname ALA GLY SER 255 | } 256 | atomselect macro medium {resname VAL THR ASP ASN PRO CYS ASX PCA HYP 257 | } 258 | atomselect macro large {protein and not (small or medium) 259 | } 260 | atomselect macro neutral {resname VAL PHE GLN TYR HIS CYS MET TRP ASX GLX PCA HYP 261 | } 262 | atomselect macro polar {protein and not hydrophobic 263 | } 264 | atomselect macro purine {resname ADE A GUA G 265 | } 266 | atomselect macro pyrimidine {resname CYT C THY T URA U 267 | } 268 | atomselect macro surface {protein and not buried 269 | } 270 | atomselect macro lipid {resname DLPE DMPC DPPC GPC LPPC PALM PC PGCL POPC POPE 271 | } 272 | atomselect macro lipids {lipid 273 | } 274 | atomselect macro ion {resname AL BA CA CAL CD CES CLA CL CO CS CU CU1 CUA HG IN IOD K MG MN3 MO3 MO4 MO5 MO6 NA NAW OC7 PB POT PT RB SOD TB TL WO4 YB ZN ZN1 ZN2 275 | } 276 | atomselect macro ions {ion 277 | } 278 | atomselect macro sugar {resname AGLC 279 | } 280 | atomselect macro solvent {not (protein or sugar or nucleic or lipid) 281 | } 282 | atomselect macro carbon {name "C.*" and not ion 283 | } 284 | atomselect macro hydrogen {name "[0-9]?H.*" 285 | } 286 | atomselect macro nitrogen {name "N.*" 287 | } 288 | atomselect macro oxygen {name "O.*" 289 | } 290 | atomselect macro sulfur {name "S.*" and not ion 291 | } 292 | atomselect macro noh {not hydrogen 293 | } 294 | atomselect macro heme {resname HEM HEME 295 | } 296 | atomselect macro conformationall {altloc "" 297 | } 298 | atomselect macro conformationA {altloc "" or altloc "A" 299 | } 300 | atomselect macro conformationB {altloc "" or altloc "B" 301 | } 302 | atomselect macro conformationC {altloc "" or altloc "C" 303 | } 304 | atomselect macro conformationD {altloc "" or altloc "D" 305 | } 306 | atomselect macro conformationE {altloc "" or altloc "E" 307 | } 308 | atomselect macro conformationF {altloc "" or altloc "F" 309 | } 310 | atomselect macro drude {type DRUD or type LP 311 | } 312 | atomselect macro unparametrized beta<1 313 | atomselect macro addedmolefacture {occupancy 0.8} 314 | # Display settings 315 | display eyesep 0.065000 316 | display focallength 2.000000 317 | display height 6.000000 318 | display distance -2.000000 319 | display projection Orthographic 320 | display nearclip set 0.500000 321 | display farclip set 10.000000 322 | display depthcue off 323 | display cuestart 0.500000 324 | display cueend 10.000000 325 | display cuestart 0.500000 326 | display cueend 10.000000 327 | display cuedensity 0.320000 328 | display cuemode Exp2 329 | display shadows off 330 | display ambientocclusion off 331 | display aoambient 0.800000 332 | display aodirect 0.300000 333 | display dof off 334 | display dof_fnumber 64.000000 335 | display dof_focaldist 0.700000 336 | mol new 15leu2x.psf type psf first 0 last -1 step 1 filebonds 1 autobonds 1 waitfor all 337 | mol addfile 15leu2x.s0.equil.dcd type dcd first 0 last -1 step 1 filebonds 1 autobonds 1 waitfor all 338 | mol addfile 15leu2x.s1.equil.dcd type dcd first 0 last -1 step 1 filebonds 1 autobonds 1 waitfor all 339 | mol addfile 15leu2x.s2.equil.dcd type dcd first 0 last -1 step 1 filebonds 1 autobonds 1 waitfor all 340 | mol addfile 15leu2x.s3.equil.dcd type dcd first 0 last -1 step 1 filebonds 1 autobonds 1 waitfor all 341 | mol addfile 15leu2x.s4.equil.dcd type dcd first 0 last -1 step 1 filebonds 1 autobonds 1 waitfor all 342 | mol addfile 15leu2x.s5.equil.dcd type dcd first 0 last -1 step 1 filebonds 1 autobonds 1 waitfor all 343 | mol addfile 15leu2x.s6.equil.dcd type dcd first 0 last -1 step 1 filebonds 1 autobonds 1 waitfor all 344 | mol addfile 15leu2x.s7.equil.dcd type dcd first 0 last -1 step 1 filebonds 1 autobonds 1 waitfor all 345 | mol addfile 15leu2x.s8.equil.dcd type dcd first 0 last -1 step 1 filebonds 1 autobonds 1 waitfor all 346 | mol addfile 15leu2x.s9.equil.dcd type dcd first 0 last -1 step 1 filebonds 1 autobonds 1 waitfor all 347 | mol delrep 0 top 348 | mol representation NewCartoon 0.300000 20.000000 4.100000 0 349 | mol color SegName 350 | mol selection {all} 351 | mol material Opaque 352 | mol addrep top 353 | mol selupdate 0 top 0 354 | mol colupdate 0 top 0 355 | mol scaleminmax top 0 0.000000 0.000000 356 | mol smoothrep top 0 0 357 | mol drawframes top 0 {now} 358 | mol clipplane center 0 0 top {0.0 0.0 0.0} 359 | mol clipplane color 0 0 top {0.5 0.5 0.5 } 360 | mol clipplane normal 0 0 top {0.0 0.0 1.0} 361 | mol clipplane status 0 0 top {0} 362 | mol clipplane center 1 0 top {0.0 0.0 0.0} 363 | mol clipplane color 1 0 top {0.5 0.5 0.5 } 364 | mol clipplane normal 1 0 top {0.0 0.0 1.0} 365 | mol clipplane status 1 0 top {0} 366 | mol clipplane center 2 0 top {0.0 0.0 0.0} 367 | mol clipplane color 2 0 top {0.5 0.5 0.5 } 368 | mol clipplane normal 2 0 top {0.0 0.0 1.0} 369 | mol clipplane status 2 0 top {0} 370 | mol clipplane center 3 0 top {0.0 0.0 0.0} 371 | mol clipplane color 3 0 top {0.5 0.5 0.5 } 372 | mol clipplane normal 3 0 top {0.0 0.0 1.0} 373 | mol clipplane status 3 0 top {0} 374 | mol clipplane center 4 0 top {0.0 0.0 0.0} 375 | mol clipplane color 4 0 top {0.5 0.5 0.5 } 376 | mol clipplane normal 4 0 top {0.0 0.0 1.0} 377 | mol clipplane status 4 0 top {0} 378 | mol clipplane center 5 0 top {0.0 0.0 0.0} 379 | mol clipplane color 5 0 top {0.5 0.5 0.5 } 380 | mol clipplane normal 5 0 top {0.0 0.0 1.0} 381 | mol clipplane status 5 0 top {0} 382 | mol rename top 15leu2x.psf 383 | set viewpoints([molinfo top]) {{{1 0 0 1.78526} {0 1 0 -7.38872} {0 0 1 1.36064} {0 0 0 1}} {{0.703934 0.71006 -0.0171548 0} {-0.118766 0.0938596 -0.988477 0} {-0.700268 0.697861 0.150401 0} {0 0 0 1}} {{0.0539526 0 0 0} {0 0.0539526 0 0} {0 0 0.0539526 0} {0 0 0 1}} {{1 0 0 0.11} {0 1 0 0.45} {0 0 1 0} {0 0 0 1}}} 384 | lappend viewplist [molinfo top] 385 | set topmol [molinfo top] 386 | # done with molecule 0 387 | foreach v $viewplist { 388 | molinfo $v set {center_matrix rotate_matrix scale_matrix global_matrix} $viewpoints($v) 389 | } 390 | foreach v $fixedlist { 391 | molinfo $v set fixed 1 392 | } 393 | unset viewplist 394 | unset fixedlist 395 | mol top $topmol 396 | unset topmol 397 | proc vmdrestoremycolors {} { 398 | color scale colors RWB {1.0 0.0 0.0} {1.0 1.0 1.0} {0.0 0.0 1.0} 399 | color scale colors BWR {0.0 0.0 1.0} {1.0 1.0 1.0} {1.0 0.0 0.0} 400 | color scale colors RGryB {1.0 0.0 0.0} {0.5 0.5 0.5} {0.0 0.0 1.0} 401 | color scale colors BGryR {0.0 0.0 1.0} {0.5 0.5 0.5} {1.0 0.0 0.0} 402 | color scale colors RGB {1.0 0.0 0.0} {0.0 1.0 0.0} {0.0 0.0 1.0} 403 | color scale colors BGR {0.0 0.0 1.0} {0.0 1.0 0.0} {1.0 0.0 0.0} 404 | color scale colors RWG {1.0 0.0 0.0} {1.0 1.0 1.0} {0.0 1.0 0.0} 405 | color scale colors GWR {0.0 1.0 0.0} {1.0 1.0 1.0} {1.0 0.0 0.0} 406 | color scale colors GWB {0.0 1.0 0.0} {1.0 1.0 1.0} {0.0 0.0 1.0} 407 | color scale colors BWG {0.0 0.0 1.0} {1.0 1.0 1.0} {0.0 1.0 0.0} 408 | color scale colors BlkW {0.0 0.0 0.0} {0.5 0.5 0.5} {1.0 1.0 1.0} 409 | color scale colors WBlk {1.0 1.0 1.0} {0.5 0.5 0.5} {0.0 0.0 0.0} 410 | color scale method RWB 411 | set colorcmds { 412 | {color Display {Background} white} 413 | {color Display {BackgroundTop} black} 414 | {color Display {BackgroundBot} blue2} 415 | {color Display {FPS} white} 416 | {color Name {C} silver} 417 | {color Name {LPA} green} 418 | {color Name {LPB} green} 419 | {color Type {LP} green} 420 | {color Type {DRUD} pink} 421 | {color Element {X} cyan} 422 | {color Element {Ac} ochre} 423 | {color Element {Ag} ochre} 424 | {color Element {Al} ochre} 425 | {color Element {Am} ochre} 426 | {color Element {Ar} ochre} 427 | {color Element {As} ochre} 428 | {color Element {At} ochre} 429 | {color Element {Au} ochre} 430 | {color Element {B} ochre} 431 | {color Element {Ba} ochre} 432 | {color Element {Be} ochre} 433 | {color Element {Bh} ochre} 434 | {color Element {Bi} ochre} 435 | {color Element {Bk} ochre} 436 | {color Element {Br} ochre} 437 | {color Element {C} silver} 438 | {color Element {Ca} ochre} 439 | {color Element {Cd} ochre} 440 | {color Element {Ce} ochre} 441 | {color Element {Cf} ochre} 442 | {color Element {Cl} ochre} 443 | {color Element {Cm} ochre} 444 | {color Element {Co} ochre} 445 | {color Element {Cr} ochre} 446 | {color Element {Cs} ochre} 447 | {color Element {Cu} ochre} 448 | {color Element {Db} ochre} 449 | {color Element {Ds} ochre} 450 | {color Element {Dy} ochre} 451 | {color Element {Er} ochre} 452 | {color Element {Es} ochre} 453 | {color Element {Eu} ochre} 454 | {color Element {F} ochre} 455 | {color Element {Fe} ochre} 456 | {color Element {Fm} ochre} 457 | {color Element {Fr} ochre} 458 | {color Element {Ga} ochre} 459 | {color Element {Gd} ochre} 460 | {color Element {Ge} ochre} 461 | {color Element {He} ochre} 462 | {color Element {Hf} ochre} 463 | {color Element {Hg} ochre} 464 | {color Element {Ho} ochre} 465 | {color Element {Hs} ochre} 466 | {color Element {I} ochre} 467 | {color Element {In} ochre} 468 | {color Element {Ir} ochre} 469 | {color Element {K} ochre} 470 | {color Element {Kr} ochre} 471 | {color Element {La} ochre} 472 | {color Element {Li} ochre} 473 | {color Element {Lr} ochre} 474 | {color Element {Lu} ochre} 475 | {color Element {Md} ochre} 476 | {color Element {Mg} ochre} 477 | {color Element {Mn} ochre} 478 | {color Element {Mo} ochre} 479 | {color Element {Mt} ochre} 480 | {color Element {Na} ochre} 481 | {color Element {Nb} ochre} 482 | {color Element {Nd} ochre} 483 | {color Element {Ne} ochre} 484 | {color Element {Ni} ochre} 485 | {color Element {No} ochre} 486 | {color Element {Np} ochre} 487 | {color Element {Os} ochre} 488 | {color Element {Pa} ochre} 489 | {color Element {Pb} ochre} 490 | {color Element {Pd} ochre} 491 | {color Element {Pm} ochre} 492 | {color Element {Po} ochre} 493 | {color Element {Pr} ochre} 494 | {color Element {Pt} ochre} 495 | {color Element {Pu} ochre} 496 | {color Element {Ra} ochre} 497 | {color Element {Rb} ochre} 498 | {color Element {Re} ochre} 499 | {color Element {Rf} ochre} 500 | {color Element {Rg} ochre} 501 | {color Element {Rh} ochre} 502 | {color Element {Rn} ochre} 503 | {color Element {Ru} ochre} 504 | {color Element {Sb} ochre} 505 | {color Element {Sc} ochre} 506 | {color Element {Se} ochre} 507 | {color Element {Sg} ochre} 508 | {color Element {Si} ochre} 509 | {color Element {Sm} ochre} 510 | {color Element {Sn} ochre} 511 | {color Element {Sr} ochre} 512 | {color Element {Ta} ochre} 513 | {color Element {Tb} ochre} 514 | {color Element {Tc} ochre} 515 | {color Element {Te} ochre} 516 | {color Element {Th} ochre} 517 | {color Element {Ti} ochre} 518 | {color Element {Tl} ochre} 519 | {color Element {Tm} ochre} 520 | {color Element {U} ochre} 521 | {color Element {V} ochre} 522 | {color Element {W} ochre} 523 | {color Element {Xe} ochre} 524 | {color Element {Y} ochre} 525 | {color Element {Yb} ochre} 526 | {color Element {Zr} ochre} 527 | {color Chain {H} blue} 528 | {color Segname {HA} blue} 529 | {color Segname {HB} red} 530 | {color Conformation {all} blue} 531 | {color Molecule {0} blue} 532 | {color Structure {3_10_Helix} blue} 533 | {color Surface {Grasp} gray} 534 | {color Labels {Springs} orange} 535 | {color Stage {Even} gray} 536 | {color Stage {Odd} silver} 537 | } 538 | foreach colcmd $colorcmds { 539 | set val [catch {eval $colcmd}] 540 | } 541 | color change rgb 0 0.0 0.0 1.0 542 | color change rgb 2 0.3499999940395355 0.3499999940395355 0.3499999940395355 543 | color change rgb 3 1.0 0.5 0.0 544 | color change rgb 4 1.0 1.0 0.0 545 | color change rgb 5 0.5 0.5 0.20000000298023224 546 | color change rgb 6 0.6000000238418579 0.6000000238418579 0.6000000238418579 547 | color change rgb 7 0.0 1.0 0.0 548 | color change rgb 9 1.0 0.6000000238418579 0.6000000238418579 549 | color change rgb 11 0.6499999761581421 0.0 0.6499999761581421 550 | color change rgb 12 0.5 0.8999999761581421 0.4000000059604645 551 | color change rgb 13 0.8999999761581421 0.4000000059604645 0.699999988079071 552 | color change rgb 14 0.5 0.30000001192092896 0.0 553 | color change rgb 15 0.5 0.5 0.75 554 | color change rgb 17 0.8799999952316284 0.9700000286102295 0.019999999552965164 555 | color change rgb 18 0.550000011920929 0.8999999761581421 0.019999999552965164 556 | color change rgb 19 0.0 0.8999999761581421 0.03999999910593033 557 | color change rgb 20 0.0 0.8999999761581421 0.5 558 | color change rgb 21 0.0 0.8799999952316284 1.0 559 | color change rgb 22 0.0 0.7599999904632568 1.0 560 | color change rgb 23 0.019999999552965164 0.3799999952316284 0.6700000166893005 561 | color change rgb 24 0.009999999776482582 0.03999999910593033 0.9300000071525574 562 | color change rgb 25 0.27000001072883606 0.0 0.9800000190734863 563 | color change rgb 26 0.44999998807907104 0.0 0.8999999761581421 564 | color change rgb 27 0.8999999761581421 0.0 0.8999999761581421 565 | color change rgb 28 1.0 0.0 0.6600000262260437 566 | color change rgb 29 0.9800000190734863 0.0 0.23000000417232513 567 | color change rgb 30 0.8100000023841858 0.0 0.0 568 | color change rgb 31 0.8899999856948853 0.3499999940395355 0.0 569 | color change rgb 32 0.9599999785423279 0.7200000286102295 0.0 570 | } 571 | vmdrestoremycolors 572 | -------------------------------------------------------------------------------- /15leu2x/input/dist_orient.colvars.in: -------------------------------------------------------------------------------- 1 | # distance vector between the two helices' centers of mass 2 | colvar { 3 | name dist 4 | width 0.25 5 | distanceVec { 6 | forceNoPBC yes 7 | group1 { 8 | psfSegID HA 9 | atomNameResidueRange CA 1-15 10 | } 11 | group2 { 12 | psfSegID HB 13 | atomNameResidueRange CA 1-15 14 | } 15 | } 16 | } 17 | 18 | 19 | # orientation of helix B 20 | colvar { 21 | name orient 22 | width 0.025 23 | orientation { 24 | atoms { 25 | psfSegID HB 26 | atomNameResidueRange CA 1-15 27 | } 28 | refPositionsFile alpha_ideal_ref.xyz 29 | } 30 | } 31 | 32 | 33 | # scalar distance (norm of "dist") 34 | colvar { 35 | name r 36 | 37 | lowerBoundary 7.0 38 | upperBoundary 20.0 39 | width 0.25 40 | 41 | distance { 42 | forceNoPBC yes 43 | group1 { 44 | psfSegID HA 45 | atomNameResidueRange CA 1-15 46 | } 47 | group2 { 48 | psfSegID HB 49 | atomNameResidueRange CA 1-15 50 | } 51 | } 52 | } 53 | -------------------------------------------------------------------------------- /15leu2x/input/drag_1d.namd: -------------------------------------------------------------------------------- 1 | # -*- tcl -*- 2 | 3 | # Steered MD simulation 4 | 5 | cv config " 6 | 7 | # This string is not Tcl code, but you can still use in here Tcl variables, 8 | # such as ${numsteps}, and bracket expansion, such as [outputEnergies]. 9 | 10 | harmonic { 11 | 12 | name drag 13 | 14 | colvars r 15 | 16 | # This force constant is in kcal/mol: to get its value relative to the 17 | # unit of each colvar, divide it by width^2 18 | forceConstant 5.0 19 | 20 | # Initial center(s) of the restraint; you can use cv update and 21 | # cv printframe in VMD to get the number for the desired starting point 22 | # (in this case, the last frame of s0) 23 | centers 10.0 24 | 25 | # Final center(s) of the restraint (first frame of s0) 26 | targetCenters 16.0 27 | 28 | # Move from center to targetCenters in these many steps 29 | targetNumSteps ${numsteps} 30 | 31 | # Record the work performed by this restraint 32 | # (it will be written in the colvars.traj file) 33 | outputAccumulatedWork yes 34 | 35 | # Write also the restraint center(s), useful to plot the work 36 | outputCenters yes 37 | 38 | # Since this is a 1D bias, we can also integrate the total forces for an 39 | # additional estimate of the PMF 40 | writeTIPMF yes 41 | }" 42 | -------------------------------------------------------------------------------- /15leu2x/input/drag_6d.namd: -------------------------------------------------------------------------------- 1 | 2 | # Set up the moving restraint: for best results, set targetNumSteps equal 3 | # to the total number of MD steps (see "run" below) 4 | cv config " 5 | harmonic { 6 | 7 | name drag 8 | 9 | colvars dist orient 10 | 11 | # This force constant is in kcal/mol: to get its value relative to the 12 | # unit of each colvar, divide it by width^2 13 | forceConstant 5.0 14 | 15 | # Initial centers of the restraint for dist and orient; 16 | # you can use cv update and cv printframe in VMD to get these numbers 17 | # for the desired starting point (in this case, last frame of s0) 18 | centers ( -5.1, 8.4, -1.3) ( 0.688, 0.025, 0.268, 0.674) 19 | 20 | # Final centers of the restraint for dist and orient (first frame of s0) 21 | targetCenters ( -3.6, 15.5, 0.0) ( 0.332, 0.121, -0.025, 0.935) 22 | 23 | # Move from centers to targetCenters in these many steps 24 | targetNumSteps ${numsteps} 25 | 26 | # Record the work performed by this restraint (it will appear in the 27 | # colvars.traj file, and may be plotted against e.g. r) 28 | outputAccumulatedWork yes 29 | }" 30 | -------------------------------------------------------------------------------- /15leu2x/input/force_helical_structure.colvars.in: -------------------------------------------------------------------------------- 1 | colvar { 2 | name hArmsd 3 | width 0.25 4 | rmsd { 5 | atoms { 6 | psfSegID HA 7 | atomNameResidueRange CA 1-15 8 | } 9 | refPositionsFile alpha_ideal_ref.xyz 10 | } 11 | } 12 | 13 | colvar { 14 | name hBrmsd 15 | width 0.25 16 | rmsd { 17 | atoms { 18 | psfSegID HB 19 | atomNameResidueRange CA 1-15 20 | } 21 | refPositionsFile alpha_ideal_ref.xyz 22 | } 23 | } 24 | 25 | harmonic { 26 | colvars hArmsd hBrmsd 27 | centers 0.0 0.0 28 | forceConstant 5.0 29 | } 30 | -------------------------------------------------------------------------------- /15leu2x/input/mtd_1d.namd: -------------------------------------------------------------------------------- 1 | # -*- tcl -*- 2 | 3 | # Metadynamics protocol 4 | 5 | cv config " 6 | 7 | # This string is not Tcl code, but you can still use in here Tcl variables, 8 | # such as ${numsteps}, and bracket expansion, such as [outputEnergies]. 9 | 10 | metadynamics { 11 | 12 | name m 13 | 14 | colvars r 15 | 16 | # Value of Gaussian height (kcal/mol) 17 | hillWeight 0.01 18 | 19 | # Value of Gaussian width (i.e. 2*sigma) in units of grid points 20 | hillWidth 1.0 21 | 22 | # Put down 5k Gaussian hills 23 | newHillFrequency [expr ${numsteps} / 5000] 24 | 25 | # Since this is a 1D bias, we can also integrate the total forces for an 26 | # additional estimate of the PMF 27 | writeTIPMF yes 28 | }" 29 | -------------------------------------------------------------------------------- /15leu2x/input/mtd_2d.namd: -------------------------------------------------------------------------------- 1 | # -*- tcl -*- 2 | 3 | # Metadynamics protocol over distance and crossing angle 4 | 5 | cv configfile packing_angles.colvars.in 6 | 7 | cv config " 8 | 9 | # This string is not Tcl code, but you can still use in here Tcl variables, 10 | # such as ${numsteps}, and bracket expansion, such as [outputEnergies]. 11 | 12 | metadynamics { 13 | 14 | name m 15 | 16 | colvars r cross_angle 17 | 18 | # Value of Gaussian height (kcal/mol) 19 | hillWeight 0.01 20 | 21 | # Value of Gaussian width (i.e. 2*sigma) in units of grid points 22 | hillWidth 1.0 23 | 24 | # Put down 5k Gaussian hills 25 | newHillFrequency [expr ${numsteps} / 5000] 26 | }" 27 | -------------------------------------------------------------------------------- /15leu2x/input/packing_angles.colvars.in: -------------------------------------------------------------------------------- 1 | 2 | # Angle of rotation around the x axis for the second helix 3 | # (the first is assumed to be fixed: check that it is) 4 | colvar { 5 | 6 | name cross_angle 7 | 8 | width 6.0 9 | 10 | lowerBoundary -180.0 11 | upperBoundary 180.0 12 | 13 | lowerWall -60.0 14 | upperWall 60.0 15 | lowerWallConstant 1.0 16 | upperWallConstant 1.0 17 | 18 | spinAngle { 19 | axis (1.0, 0.0, 0.0) 20 | atoms { 21 | psfSegID HA 22 | atomNameResidueRange CA 1-15 23 | } 24 | refPositionsFile alpha_ideal_ref.xyz 25 | } 26 | } 27 | 28 | 29 | # Angle of rotation around z axis (keep phase of the helix) 30 | colvar { 31 | 32 | name phase_angle 33 | 34 | width 6.0 35 | 36 | spinAngle { 37 | axis (0.0, 0.0, 1.0) 38 | atoms { 39 | psfSegID HB 40 | atomNameResidueRange CA 1-15 41 | 42 | } 43 | refPositionsFile alpha_ideal_ref.xyz 44 | } 45 | } 46 | -------------------------------------------------------------------------------- /15leu2x/input/plot_colvars_traj.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python 2 | 3 | # Select variables from a Colvars trajectory file and optionally plot them as 4 | # a 1D graph as a function of time or of one of the variables. 5 | 6 | # Source: https://github.com/colvars/colvars/blob/master/colvartools/plot_colvars_traj.py?raw=true 7 | 8 | from __future__ import print_function 9 | 10 | import os 11 | import sys 12 | 13 | if (sys.version_info[:2] < (2, 7)): 14 | # Save some explanations 15 | print("Python versions prior to 2.7 are no longer supported.") 16 | sys.exit(1) 17 | 18 | import numpy as np 19 | 20 | 21 | class Colvar_traj(object): 22 | """ 23 | Class to store the trajectory of a collective variable. 24 | The series of step numbers are included, because collective 25 | variables may be added or deleted during the simulation. 26 | """ 27 | 28 | _name = "" 29 | _step = np.empty(shape=(0)) 30 | _colvar = np.empty(shape=(0)) 31 | 32 | def __init__(self, name): 33 | """Sets the name of the variable""" 34 | self._name = name 35 | self._step = np.zeros(shape=(0), dtype=np.int64) 36 | self._colvar = np.zeros(shape=(0), dtype=np.float) 37 | 38 | def __len__(self): 39 | """Returns the length of the trajectory""" 40 | return len(self._step) 41 | 42 | @property 43 | def num_dimensions(self): 44 | s = self._colvar.shape 45 | if (len(s) > 1): 46 | return s[1] 47 | else: 48 | return 1 49 | 50 | def set_num_dimensions(self, n_d): 51 | """Set the number of components of the collective variable""" 52 | if (len(self) > 0): 53 | print("Warning: changing the number of dimensions " 54 | "of collective variable \""+self._name+ 55 | "\" after it has already been read.") 56 | if (n_d > 1): 57 | self._colvar.resize((len(self), n_d)) 58 | else: 59 | self._colvar.resize((len(self))) 60 | 61 | def resize(self, n): 62 | """Change the number of records in the trajectory""" 63 | self._step.resize((n)) 64 | if (len(self._colvar.shape) > 1): 65 | self._colvar.resize((n, self._colvar.shape[1])) 66 | else: 67 | self._colvar.resize((n)) 68 | 69 | 70 | @property 71 | def name(self): 72 | """Returns the name of the collective variable""" 73 | return self._name 74 | @property 75 | def steps(self): 76 | """Returns the array of step numbers""" 77 | return self._step 78 | @property 79 | def values(self): 80 | """Returns the array of collective variable values""" 81 | return self._colvar 82 | 83 | 84 | class Colvars_traj(object): 85 | """Trajectories of collective variables (read from colvars.traj file)""" 86 | 87 | _keys = [] 88 | _start = {} 89 | _end = {} 90 | _colvars = {} 91 | _found = {} 92 | _count = -1 93 | _frame = -1 94 | 95 | def __init__(self): 96 | self._keys = ['step'] 97 | self._start['step'] = 0 98 | self._end['step'] = -1 99 | self._count = 0 100 | self._frame = 0 101 | 102 | def __getitem__(self, key): 103 | return self._colvars[key] 104 | 105 | def __contains__(self, key): 106 | return key in self._colvars 107 | 108 | @property 109 | def num_frames_read(self): 110 | """Number of trajectory frames read so far""" 111 | return self._count 112 | 113 | @property 114 | def num_frames(self): 115 | """Number of trajectory frames processed""" 116 | return self._frame 117 | 118 | @property 119 | def variables(self): 120 | """Names of variables defined""" 121 | return self._keys[1:] # The first entry is "step" 122 | 123 | def parse_comment_line(self, line): 124 | """ 125 | Read in a comment line from a colvars.traj file and update the names of 126 | collective variables if needed. 127 | """ 128 | new_keys = (line[1:]).split() # skip the hash char 129 | if (not self._keys == ['step'] and self._colvars != {}): 130 | if (new_keys != self._keys): 131 | print("Info: Configuration changed; the new entries are: ") 132 | print(new_keys) 133 | self._keys = new_keys 134 | if (self._keys[0] != 'step'): 135 | raise KeyError("Error: file format incompatible with colvars.traj") 136 | # Find the boundaries of each column 137 | for i in range(1, len(self._keys)): 138 | self._start[self._keys[i]] = line.find(' '+self._keys[i]) 139 | self._end[self._keys[i-1]] = line.find(' '+self._keys[i]) 140 | self._end[self._keys[-1]] = -1 141 | 142 | def parse_line(self, line): 143 | """ 144 | Read in a data line from a colvars.traj file 145 | """ 146 | 147 | step = np.int64(line[0:self._end['step']]) 148 | 149 | for v in self._keys[1:]: 150 | text = line[self._start[v]:self._end[v]] 151 | v_v = np.fromstring(text.lstrip(' (').rstrip(') '), sep=',') 152 | n_d = len(v_v) 153 | if (v not in self._colvars): 154 | self._colvars[v] = Colvar_traj(v) 155 | self._colvars[v].set_num_dimensions(n_d) 156 | cv = self._colvars[v] 157 | n = len(cv) 158 | cv.resize(n+1) 159 | cv.steps[n] = step 160 | cv.values[n] = v_v 161 | 162 | self._count += 1 163 | 164 | def read_files(self, filenames, list_variables=False, 165 | first=0, last=-1, every=1): 166 | """ 167 | Read a series of colvars.traj files. 168 | filenames : list of strings 169 | list of file names 170 | list_variables : bool 171 | list variable names to screen 172 | first : int 173 | index of first record to read in (see also mol load in VMD) 174 | last : int 175 | index of last record to read in 176 | every : int 177 | read every these many records 178 | """ 179 | last = np.int64(last) 180 | if (last == -1): 181 | last = np.int64(np.iinfo(np.int64).max) 182 | last_step = -1 183 | for f in filenames: 184 | for line in f: 185 | if (len(line) == 0): continue 186 | if (line[:1] == "@"): continue # xmgr file metadata 187 | if (line[:1] == "#"): 188 | self.parse_comment_line(line) 189 | continue 190 | if (args.list_variables): 191 | for v in self.variables: 192 | print(v) 193 | return 194 | step = np.int64(line[0:self._end['step']]) 195 | if (step == last_step): continue 196 | if ((self._frame >= first) and (self._frame <= last) and 197 | (self._frame % every == 0)): 198 | self.parse_line(line) 199 | self._frame += 1 200 | last_step = step 201 | 202 | 203 | if (__name__ == '__main__'): 204 | 205 | import argparse 206 | 207 | parser = \ 208 | argparse.ArgumentParser(description='Select variables from a Colvars ' 209 | 'trajectory file and optionally plot them ' 210 | 'as a 1D graph as a function of time or of ' 211 | 'one of the variables.', \ 212 | formatter_class=argparse.ArgumentDefaultsHelpFormatter) 213 | 214 | parser.add_argument(dest='filenames', 215 | nargs='*', 216 | type=argparse.FileType('r'), 217 | help='Space-separated list of input files ' 218 | '(will be concatenated)', 219 | default=[]) 220 | 221 | parser.add_argument('--dt', 222 | dest='dt', 223 | type=float, 224 | help='Integration time step', 225 | default=2.0e-6) 226 | 227 | parser.add_argument('--first-frame', 228 | dest='first', 229 | type=np.int64, 230 | help='First frame to read', 231 | default=0) 232 | 233 | parser.add_argument('--last-frame', 234 | dest='last', 235 | type=np.int64, 236 | help='Last frame to read', 237 | default=-1) 238 | 239 | parser.add_argument('--skip-frames', 240 | dest='skip', 241 | type=np.int64, 242 | help='Read every these many frames', 243 | default=1) 244 | 245 | parser.add_argument('--variables', 246 | dest='variables', 247 | nargs='*', 248 | type=str, 249 | help='Space-separated list of names of collective ' 250 | 'variables to write or plot.', 251 | default=[]) 252 | 253 | parser.add_argument('--list-variables', 254 | dest='list_variables', 255 | action='store_true', 256 | help='List all names of collective variables ' 257 | 'defined up until the first line of data.', 258 | default=False) 259 | 260 | parser.add_argument('--output-file', 261 | dest='output_file', 262 | type=str, 263 | help='Write the selected variables to a text file. ' 264 | 'The step number is always included as the first ' 265 | 'column, and all variables ' 266 | 'must be defined on the same trajectory segments.', 267 | default=None) 268 | 269 | try: 270 | import matplotlib 271 | matplotlib.use('Agg') 272 | import matplotlib.pyplot as plt 273 | from matplotlib.backends.backend_pdf import PdfPages 274 | matplotlib.rcParams['font.size'] = 10 275 | 276 | parser.add_argument('--plot', 277 | dest='plot', 278 | type=str, 279 | help='Plot the variables in a PDF file ' 280 | 'prefixed by this string.', 281 | default=None) 282 | 283 | parser.add_argument('--plot-x-axis', 284 | dest='plot_x_axis', 285 | type=str, 286 | help='Use this variable as X axis in the plot.', 287 | default='time') 288 | 289 | parser.add_argument('--plot-x-label', 290 | dest='plot_x_label', 291 | type=str, 292 | help='Use this label for the X axis.', 293 | default=None) 294 | 295 | parser.add_argument('--plot-y-label', 296 | dest='plot_y_label', 297 | type=str, 298 | help='Use this label for the Y axis.', 299 | default=None) 300 | 301 | parser.add_argument('--plot-keys', 302 | dest='plot_keys', 303 | nargs='*', 304 | type=str, 305 | help='Alternative names for the legend', 306 | default=[]) 307 | 308 | except: 309 | pass 310 | 311 | args = parser.parse_args() 312 | 313 | if (len(args.filenames) == 0): 314 | raise Exception("No filenames provided.") 315 | 316 | colvars_traj = Colvars_traj() 317 | colvars_traj.read_files(args.filenames, 318 | list_variables=args.list_variables, 319 | first=args.first, 320 | last=args.last, 321 | every=args.skip) 322 | 323 | if (args.list_variables): 324 | sys.exit() 325 | 326 | variables = args.variables 327 | if (len(variables) == 0): variables = colvars_traj.variables 328 | 329 | plot_keys = dict(zip(variables, variables)) 330 | if (len(args.plot_keys)): 331 | if (len(args.plot_keys) != len(variables)): 332 | raise KeyError("--plot-keys must be as long " 333 | "as the number of variables.") 334 | else: 335 | plot_keys = dict(zip(variables, args.plot_keys)) 336 | time_unit = args.dt 337 | 338 | 339 | if (args.output_file): 340 | 341 | fmt = " %12d" 342 | columns = [colvars_traj[variables[0]].steps] 343 | for var in variables: 344 | cv = colvars_traj[var] 345 | for ic in range(cv.num_dimensions): 346 | y = cv.values 347 | if (cv.num_dimensions > 1): 348 | y = cv.values[ic] 349 | columns += [y] 350 | fmt += " %21.14f" 351 | columns = tuple(columns) 352 | np.savetxt(fname=args.output_file, 353 | X=list(zip(*columns)), 354 | fmt=str(fmt)) 355 | 356 | 357 | if (args.plot): 358 | 359 | lowercase = args.plot.lower() 360 | if (lowercase[-4:] == '.pdf'): 361 | args.plot = args.plot[:-4] 362 | 363 | pdf = PdfPages(args.plot+'.pdf') 364 | fig = plt.figure(figsize=(3.0, 3.0)) 365 | if (args.plot_x_label): plt.xlabel(args.plot_x_label) 366 | if (args.plot_y_label): plt.ylabel(args.plot_y_label) 367 | 368 | for var in variables: 369 | 370 | cv = colvars_traj[var] 371 | 372 | x = cv.steps 373 | if (args.plot_x_axis == 'time'): 374 | x = cv.steps * time_unit 375 | elif (args.plot_x_axis == 'step'): 376 | x = cv.steps 377 | else: 378 | x = colvars_traj[args.plot_x_axis].values 379 | 380 | for ic in range(cv.num_dimensions): 381 | y = cv.values 382 | if (cv.num_dimensions > 1): 383 | y = cv.values[ic] 384 | plt.plot(x, y, '-', 385 | label=plot_keys[var], 386 | alpha=0.5) 387 | 388 | plt.legend(loc='upper left') 389 | plt.tight_layout() 390 | 391 | pdf.savefig() 392 | pdf.close() 393 | 394 | -------------------------------------------------------------------------------- /15leu2x/input/quaternion2rmatrix.tcl: -------------------------------------------------------------------------------- 1 | proc quaternion_to_matrix { quaternion_string } { 2 | 3 | # this function returns the rotation matrix R(q) as a function of the 4 | # quaternion q; 5 | # q is provided as a string, in the format of the collective 6 | # variables module: (q0, q1, q2, q3) 7 | 8 | # if set to a non-zero value, the function returns a 4x4 matrix suitable for 9 | # being used in VMD; otherwise, a regular 3x3 matrix 10 | set vmd_format 1 11 | 12 | set quat_args [split ${quaternion_string} " ,()"] 13 | set quat_args_parsed [list] 14 | foreach arg ${quat_args} { 15 | if { ${arg} != "" } { 16 | lappend quat_args_parsed ${arg} 17 | } 18 | } 19 | 20 | set q0 [lindex ${quat_args_parsed} 0] 21 | set q1 [lindex ${quat_args_parsed} 1] 22 | set q2 [lindex ${quat_args_parsed} 2] 23 | set q3 [lindex ${quat_args_parsed} 3] 24 | 25 | if { ${vmd_format} } { 26 | return [list \ 27 | [list [expr ${q0}*${q0} + ${q1}*${q1} - ${q2}*${q2} - ${q3}*${q3}] [expr 2.0 * (${q1}*${q2} - ${q0}*${q3})] [expr 2.0 * (${q0}*${q2} + ${q1}*${q3})] 0.0] \ 28 | [list [expr 2.0 * (${q0}*${q3} + ${q1}*${q2})] [expr ${q0}*${q0} - ${q1}*${q1} + ${q2}*${q2} - ${q3}*${q3}] [expr 2.0 * (${q2}*${q3} - ${q0}*${q1})] 0.0] \ 29 | [list [expr 2.0 * (${q1}*${q3} - ${q0}*${q2})] [expr 2.0 * (${q0}*${q1} + ${q2}*${q3})] [expr ${q0}*${q0} - ${q1}*${q1} - ${q2}*${q2} + ${q3}*${q3}] 0.0] \ 30 | [list 0.0 0.0 0.0 1.0] \ 31 | ] 32 | } else { 33 | return [list \ 34 | [list [expr ${q0}*${q0} + ${q1}*${q1} - ${q2}*${q2} - ${q3}*${q3}] [expr 2.0 * (${q1}*${q2} - ${q0}*${q3})] [expr 2.0 * (${q0}*${q2} + ${q1}*${q3})]] \ 35 | [list [expr 2.0 * (${q0}*${q3} + ${q1}*${q2})] [expr ${q0}*${q0} - ${q1}*${q1} + ${q2}*${q2} - ${q3}*${q3}] [expr 2.0 * (${q2}*${q3} - ${q0}*${q1})]] \ 36 | [list [expr 2.0 * (${q1}*${q3} - ${q0}*${q2})] [expr 2.0 * (${q0}*${q1} + ${q2}*${q3})] [expr ${q0}*${q0} - ${q1}*${q1} - ${q2}*${q2} + ${q3}*${q3}]] \ 37 | ] 38 | } 39 | 40 | } 41 | -------------------------------------------------------------------------------- /15leu2x/input/restrain_helixA.colvars.in: -------------------------------------------------------------------------------- 1 | # Define the absolute position of the helix A as distance vector from the 2 | # origin and the orientation as rotation from the reference structure 3 | 4 | 5 | colvar { 6 | name hApos 7 | width 0.25 8 | distanceVec { 9 | forceNoPBC yes 10 | group1 { 11 | psfSegID HA 12 | atomNameResidueRange CA 1-15 13 | } 14 | group2 { 15 | dummyAtom (0.0, 0.0, 0.0) 16 | } 17 | } 18 | } 19 | 20 | 21 | colvar { 22 | name hAorient 23 | width 0.05 24 | orientation { 25 | atoms { 26 | psfSegID HA 27 | atomNameResidueRange CA 1-15 28 | } 29 | refPositionsFile alpha_ideal_ref.xyz 30 | } 31 | } 32 | 33 | 34 | harmonic { 35 | colvars hApos hAorient 36 | centers (0.0, 0.0, 0.0) (1.0, 0.0, 0.0, 0.0) 37 | forceConstant 5.0 38 | } 39 | -------------------------------------------------------------------------------- /15leu2x/input/show_rotation_axis.tcl: -------------------------------------------------------------------------------- 1 | #play colvar_display.tcl 2 | #start_colvar_display dist 3 | stop_colvar_display 4 | start_rotation_display orient 5 | 6 | -------------------------------------------------------------------------------- /15leu2x/input/show_variables.tcl: -------------------------------------------------------------------------------- 1 | play colvar_display.tcl 2 | start_colvar_display -------------------------------------------------------------------------------- /15leu2x/input/unbind.namd: -------------------------------------------------------------------------------- 1 | # -*- tcl -*- 2 | 3 | set numsteps 50000 4 | 5 | # If the environment variable starting_structure is not set, the script 6 | # defaults to the value written below 7 | if { [info exists env(starting_structure)] } { 8 | set starting_structure $env(starting_structure) 9 | } else { 10 | set starting_structure "s0" 11 | } 12 | 13 | # Set the name of this job based on the name of this script 14 | set job 15leu2x.${starting_structure}.[file rootname [file tail [info script]]] 15 | 16 | 17 | # Input 18 | 19 | # Physical description 20 | paraTypeCharmm on 21 | structure 15leu2x.psf 22 | parameters par_all36_prot.prm ; # CHARMM36 force field parameters 23 | 1-4scaling 1.0 24 | exclude scaled1-4 25 | rigidBonds all 26 | useSettle on 27 | 28 | # Cutoffs and approximations 29 | switchdist 10.0 30 | cutoff 12.0 31 | pairlistdist 13.5 32 | stepspercycle 20 33 | timestep 2.0 34 | 35 | # Initial data and boundary conditions 36 | 37 | coordinates 15leu2x.s0.pdb ; # One is as good as another 38 | if { [info exists starting_structure] } { 39 | binCoordinates 15leu2x.${starting_structure}.equil.coor 40 | } 41 | 42 | COMmotion no 43 | zeroMomentum yes 44 | seed 87654321 45 | 46 | # Thermodynamic ensemble 47 | temperature 0.0 48 | langevin on 49 | langevinTemp 300.0 50 | langevinDamping 10.0 51 | 52 | # Output 53 | 54 | # Main output and restarts 55 | outputName ${job} 56 | binaryOutput yes 57 | restartName ${job} 58 | restartFreq 5000 59 | binaryRestart yes 60 | 61 | # Trajectory output 62 | DCDfile ${job}.dcd 63 | DCDfreq 500 64 | DCDUnitCell yes 65 | 66 | # Standard output frequencies 67 | outputEnergies 500 68 | outputMomenta 500 69 | outputTiming 500 70 | 71 | 72 | # Enable the collective variables module (Colvars) 73 | colvars on 74 | 75 | # Load main Colvars configuration: it can be all contained in this file, 76 | # but we are doing it in pieces to control what to load 77 | cv configfile dist_orient.colvars.in 78 | 79 | # Hold helix A in place, so that variables can be computed in a consistent 80 | # frame of reference: note that these restraints apply only to the center of 81 | # mass and orientation of helix A, and unlike position restraints they won't 82 | # affect its internal dynamics 83 | cv configfile restrain_helixA.colvars.in 84 | 85 | # # Optional: Restrain both peptides to be helical at all times 86 | # cv configfile force_helical_structure.colvars.in 87 | 88 | 89 | # Protocol for a 1D SMD simulation (also includes TI PMF calculation) 90 | source drag_1d.namd 91 | 92 | # # Alternative: protocol for a 6D SMD simulation 93 | # source drag_6d.namd 94 | 95 | # # Alternative: protocol for a 1D metadynamics simulation 96 | # source mtd_1d.namd 97 | 98 | # # Alternative: protocol for a 1D ABF simulation 99 | # source abf.namd 100 | 101 | # # Alternative: protocol for a 2D metadynamics simulation (you may want to 102 | # # increase numsteps) 103 | # source mtd_2d.namd 104 | 105 | 106 | # Execute the MD run 107 | run ${numsteps} 108 | 109 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | Use the clone/download button to download the input deck as a Tar or Zip file. 2 | 3 | Additional data sets (DCD files) are available at: 4 | https://github.com/Colvars/datasets 5 | and can be unpacked in the current folder. 6 | -------------------------------------------------------------------------------- /symmetric_DBC/AFEP.colvars: -------------------------------------------------------------------------------- 1 | colvarsTrajFrequency 100 2 | colvarsRestartFrequency 100000 3 | 4 | colvar { 5 | name DBC_sym 6 | 7 | # Grid parameters for histogramming 8 | width 0.1 9 | lowerboundary 0.0 10 | upperboundary 2.5 11 | 12 | rmsd { 13 | refPositionsFile ref.pdb 14 | atomPermutation {16214 16209 16210 16211 16212 16213} 15 | atomPermutation {16213 16214 16209 16210 16211 16212} 16 | atomPermutation {16212 16213 16214 16209 16210 16211} 17 | atomPermutation {16211 16212 16213 16214 16209 16210} 18 | atomPermutation {16210 16211 16212 16213 16214 16209} 19 | atomPermutation {16210 16209 16214 16213 16212 16211} 20 | atomPermutation {16211 16210 16209 16214 16213 16212} 21 | atomPermutation {16212 16211 16210 16209 16214 16213} 22 | atomPermutation {16213 16212 16211 16210 16209 16214} 23 | atomPermutation {16214 16213 16212 16211 16210 16209} 24 | atomPermutation {16209 16214 16213 16212 16211 16210} 25 | atoms { 26 | atomNumbers {16209 16210 16211 16212 16213 16214} 27 | # Moving frame of reference 28 | centerReference yes 29 | rotateReference yes 30 | fittingGroup { 31 | # Define binding site atoms used for fitting 32 | atomNumbers {19 90 1087 1099 1115 1127 1137 1147 1163 1187 1194 1213 1232 1256 1270 1280 1302 1321 1345 1357 1373 1394 1406 1417 1436 1448 1458 1474 1498 1522 1533 1543 1553 1572 1586 1603 1619 1639 1656 1673 1680 1696 1710 1717 1733 1743 1750 1770 1784 1798 1814 1833 1857 1874 1893 1910 1927 1949 1973 1997 2009 2024 2034 2044 2060 2074 2093 2103 2125 2160 2184 2296 2306 2328 2352 2368 2387 2401 2415 2435 2459 2473} 33 | } 34 | # Reference coordinates for binding site atoms 35 | # (can be the same file as ligand coordinates above) 36 | refPositionsFile ref.pdb # PDB or XYZ file 37 | } 38 | } 39 | } 40 | 41 | 42 | colvar { 43 | name protein_rotation 44 | 45 | orientation { 46 | # Reference coordinates (for protein) 47 | refpositionsfile ref.pdb 48 | atoms { 49 | # Protein atoms used for optimal rotation 50 | atomNumbers {5 19 38 58 73 90 109 133 152 164 179 186 205 229 248 270 289 310 332 344 354 369 376 397 418 432 451 458 477 484 501 520 539 553 575 588 600 612 631 645 655 665 687 698 713 732 744 766 776 795 802 826 840 851 865 872 888 907 921 943 955 970 980 995 1017 1036 1056 1070 1087 1099 1115 1127 1137 1147 1163 1187 1194 1213 1232 1256 1270 1280 1302 1321 1345 1357 1373 1394 1406 1417 1436 1448 1458 1474 1498 1522 1533 1543 1553 1572 1586 1603 1619 1639 1656 1673 1680 1696 1710 1717 1733 1743 1750 1770 1784 1798 1814 1833 1857 1874 1893 1910 1927 1949 1973 1997 2009 2024 2034 2044 2060 2074 2093 2103 2125 2136 2160 2184 2205 2219 2236 2248 2260 2272 2296 2306 2328 2352 2368 2387 2401 2415 2435 2459 2473 2480} 51 | } 52 | } 53 | } 54 | 55 | 56 | # Harmonic restraint to prevent protein rotation 57 | 58 | harmonic { 59 | colvars protein_rotation 60 | # Quaternion components are <= 1, so force constant unit is very small 61 | forceConstant 10000.0 62 | centers (1.0, 0.0, 0.0, 0.0) 63 | } 64 | 65 | # Flat-bottom harmonic restraint on DBC 66 | 67 | harmonicWalls { 68 | colvars DBC_sym 69 | upperWalls 1.5 70 | forceConstant 200 71 | } 72 | 73 | # Histogram analysis 74 | 75 | histogram { 76 | colvars DBC_sym 77 | } 78 | -------------------------------------------------------------------------------- /symmetric_DBC/README.md: -------------------------------------------------------------------------------- 1 | # Example Colvars configuration for symmetric Distance-to-Bound-configuration (DBC) coordinate 2 | 3 | This can be used as binding restraint to compute the binding affinity of a symmetric ligand. 4 | (references coming soon) 5 | 6 | # How to adapt the inputs to a different system 7 | 8 | ## Colvars for alchemical perturbation in the receptor 9 | 10 | 1. Start from `AFEP.colvars`; 11 | 2. Open the reference structure of the receptor-ligand complex in VMD; 12 | 3. Using the Colvars Dashobard, adapt the atom group definitions; 13 | 4. Adapt the `atomPermutation` lines to describe ligand symmetry; 14 | 5. Run an MD simulation of the bound state with the histogram blocks of `AFEP.colvars` enabled, but not the restraints; 15 | 6. Compute the upper threshold for the DBC coordinate from that simulation and set the `upperWall` restraint accordingly. 16 | 17 | ## Colvars for restraint free energy perturbation in gas phase 18 | 19 | 1. Start from `RFEP_vacuum.colvars`; 20 | 2. Open the structure of the ligand in gas phase in VMD; 21 | 3. Using the Colvars Dashboard, adapt the atom group definition for the ligand as dont for the full structure above; 22 | 4. Adjust the `atomPermutation` lines defined above to the atom numbers in the gas phase ligand structure; 23 | 5. Set the center of the COM restraint (`dummyAtom` in `RFEP_vacuum.colvars`) by computing the `ligand_COM` coordinate in the reference structure. 24 | -------------------------------------------------------------------------------- /symmetric_DBC/RFEP_vacuum.colvars: -------------------------------------------------------------------------------- 1 | colvarsTrajFrequency 100 2 | colvarsRestartFrequency 100000 3 | 4 | colvar { 5 | name DBC_sym 6 | 7 | rmsd { 8 | refPositionsFile ref_vacuum.pdb 9 | atomPermutation {6 1 2 3 4 5} 10 | atomPermutation {5 6 1 2 3 4} 11 | atomPermutation {4 5 6 1 2 3} 12 | atomPermutation {3 4 5 6 1 2} 13 | atomPermutation {2 3 4 5 6 1} 14 | atomPermutation {2 1 6 5 4 3} 15 | atomPermutation {3 2 1 6 5 4} 16 | atomPermutation {4 3 2 1 6 5} 17 | atomPermutation {5 4 3 2 1 6} 18 | atomPermutation {6 5 4 3 2 1} 19 | atomPermutation {1 6 5 4 3 2} 20 | atoms { 21 | atomNumbers {1 2 3 4 5 6} 22 | # Moving frame of reference is defined below 23 | centerReference off 24 | rotateReference off 25 | # Reference coordinates for binding site atoms 26 | # (can be the same file as ligand coordinates above) 27 | } 28 | } 29 | } 30 | 31 | 32 | colvar { 33 | name COM_distance 34 | 35 | distance { 36 | group1 { # Ligand positions 37 | atomNumbers {1 2 3 4 5 6} 38 | # Gas phase -> Fixed frame of reference 39 | } 40 | 41 | group2 { # Reference ligand COM position 42 | # Measure ligand_COM colvar below in ref structure to find optimal value 43 | dummyAtom (-2.121, 5.272, 9.564) 44 | } 45 | } 46 | } 47 | 48 | 49 | colvar { 50 | # Auxiliary colvar to find the ligand COM in reference structure 51 | name ligand_COM 52 | 53 | distanceVec { 54 | group2 { # Ligand positions 55 | atomNumbers {1 2 3 4 5 6} 56 | # Gas phase -> Fixed frame of reference 57 | } 58 | 59 | group1 { 60 | dummyAtom (0, 0, 0) 61 | } 62 | } 63 | } 64 | 65 | # Changing flat-bottom harmonic restraint on DBC 66 | 67 | harmonicWalls { 68 | colvars DBC_sym 69 | 70 | upperWalls 1.5 71 | forceConstant 0.0 72 | targetForceConstant 200.0 73 | targetForceExponent 6.0 74 | 75 | targetEquilSteps 5000 76 | lambdaSchedule 1.00 0.95 0.90 0.85 0.80 0.75 0.70 0.65 0.60 0.55 0.50 0.45 0.40 0.35 0.30 0.25 0.20 0.15 0.10 0.05 0.00 77 | targetNumSteps 1000000 78 | } 79 | 80 | 81 | # Background flat-bottom harmonic restraint on COM 82 | 83 | harmonicWalls { 84 | colvars COM_distance 85 | upperWalls 1.5 86 | forceConstant 200 87 | } 88 | -------------------------------------------------------------------------------- /symmetric_DBC/ref_vacuum.pdb: -------------------------------------------------------------------------------- 1 | CRYST1 0.000 0.000 0.000 90.00 90.00 90.00 P 1 1 2 | ATOM 1 C1 BNZ H 200 -2.070 3.968 10.077 0.00 0.00 HETA 3 | ATOM 2 C2 BNZ H 200 -2.585 4.220 8.814 0.00 0.00 HETA 4 | ATOM 3 C3 BNZ H 200 -2.640 5.516 8.287 0.00 0.00 HETA 5 | ATOM 4 C4 BNZ H 200 -2.180 6.577 9.052 0.00 0.00 HETA 6 | ATOM 5 C5 BNZ H 200 -1.651 6.312 10.313 0.00 0.00 HETA 7 | ATOM 6 C6 BNZ H 200 -1.600 5.036 10.839 0.00 0.00 HETA 8 | ATOM 7 H1 BNZ H 200 -2.035 2.961 10.464 0.00 0.00 HETA 9 | ATOM 8 H2 BNZ H 200 -2.951 3.395 8.222 0.00 0.00 HETA 10 | ATOM 9 H3 BNZ H 200 -3.036 5.686 7.297 0.00 0.00 HETA 11 | ATOM 10 H4 BNZ H 200 -2.231 7.589 8.678 0.00 0.00 HETA 12 | ATOM 11 H5 BNZ H 200 -1.268 7.133 10.901 0.00 0.00 HETA 13 | ATOM 12 H6 BNZ H 200 -1.200 4.867 11.827 0.00 0.00 HETA 14 | END 15 | -------------------------------------------------------------------------------- /tma-aco/Common/charmm/par_all35_ethers.prm: -------------------------------------------------------------------------------- 1 | *>>>>>>>>>>>>>>>>> All-hydrogen parameters <<<<<<<<<<<<<<<<<<<<<<< 2 | *>>>>>>>>>>>>>>>> CHARMM32 ether force field <<<<<<<<<<<<<<<<<<<<< 3 | *>>>>>>>>>>>>>>>>>>>>>> December 2006 <<<<<<<<<<<<<<<<<<<<<<<<<<<< 4 | *>>>>>>>> Direct comments to Alexander D. MacKerell Jr. <<<<<<<<<< 5 | *>>>>>>>>>>>> via the CHARMM forum: www.charmm.org <<<<<<<<<<<<<<< 6 | * 7 | 8 | !Vorobyov, I., Anisimov, V.M., Greene, S., Venable, R.M., Moser, A., 9 | !Pastor, R.W., and MacKerell, A.D., Jr. "Additive and Classical Drude 10 | !Polarizable Force Fields for Linear and Cyclic Ethers," Journal of 11 | !Chemical Theory and Computing, 3: 1120-1133, 2007 12 | ! 13 | ! O-C-C-O torsion modified; HK Lee, RM Venable, RW Pastor August 2007 14 | ! 15 | !Hwankyu Lee, Richard M Venable, Alexander D MacKerell Jr., Richard W Pastor 16 | !Molecular dynamics studies of polyethylene oxide and polyethylene glycol: 17 | !Hydrodynamic radius and shape anisotropy 18 | !Biophysical J., 95: 1590-1599, 2008 19 | ! 20 | ! ********* V(bond) = Kb(b - b0)**2 21 | ATOMS 22 | MASS -1 HCA1A 1.00800 ! Alkane H attached to C(sp3)H (eq. HA1) 23 | MASS -1 HCA2A 1.00800 ! Alkane H attached to C(sp3)H2 (eq. HA2) 24 | MASS -1 HCA3A 1.00800 ! Alkane H attached to C(sp3)H3 (eq. HA3) 25 | MASS -1 HCA25A 1.00800 ! Alkane H attached to C(sp3)H2 in 5-membered ring 26 | MASS -1 CC30A 12.01100 ! -C(sp3) Carbon (eq. CT) 27 | MASS -1 CC31A 12.01100 ! -C(sp3)H Carbon (eq. CT1) 28 | MASS -1 CC32A 12.01100 ! -C(sp3)H2 Carbon (eq. CT2) 29 | MASS -1 CC33A 12.01100 ! -C(sp3)H3 Carbon (eq. CT3) 30 | MASS -1 CC325A 12.01100 ! -C(sp3)H2 Carbon in 5-membered ring 31 | MASS -1 CC325B 12.01100 ! -C(sp3)H2 Carbon in THF (tetrahydrofuran) 32 | MASS -1 CC326A 12.01100 ! -C(sp3)H2 Carbon in THP (tetrahydropyran) 33 | MASS -1 OC30A 15.99940 ! Ether Oxygen 34 | MASS -1 OC305A 15.99940 ! Ether Oxygen in THF 35 | 36 | BONDS 37 | !! Alkane standard C27 parameeters. Not modified from original. 38 | CC31A HCA1A 309.00 1.111 ! alkanes, 4/98 39 | CC32A HCA2A 309.00 1.111 ! alkanes, 4/98 40 | CC33A HCA3A 322.00 1.111 ! alkanes, 4/98 41 | CC30A CC32A 222.50 1.538 ! 10/98 42 | CC30A CC33A 222.50 1.538 ! 10/98 43 | CC31A CC31A 222.50 1.500 ! alkanes, 3/92 44 | CC31A CC32A 222.50 1.538 ! alkanes, 3/92 45 | CC31A CC33A 222.50 1.538 ! alkanes, 3/92 46 | CC32A CC32A 222.50 1.530 ! alkanes, 3/92 47 | CC32A CC33A 222.50 1.528 ! alkanes, 3/92 48 | CC33A CC33A 222.50 1.530 ! alkanes, 3/92 49 | CC325A CC325A 195.00 1.548 ! cyclopentane CPEN 10/17/05 viv 50 | CC325A HCA25A 307.00 1.116 ! cyclopentane CPEN 10/17/05 viv 51 | CC325B OC305A 350.00 1.425 ! THF, nucleotide CSD/NDB survey, 5/30/06,viv 52 | CC325B CC325B 195.00 1.518 ! THF, nucleotide CSD/NDB survey, 5/30/06,viv 53 | CC325B HCA25A 307.00 1.100 ! THF, THF neutron diffr., 5/30/06, viv 54 | CC325B CC33A 222.50 1.528 ! TF2M, viv 55 | CC32A OC30A 360.00 1.415 ! DEET, diethylether, alex 56 | CC33A OC30A 360.00 1.415 ! DEET, diethylether, alex 57 | CC326A HCA2A 309.00 1.111 ! THP, viv 58 | CC326A CC326A 222.50 1.530 ! THP, viv 59 | CC326A OC30A 360.00 1.415 ! DEET, diethylether, viv 60 | 61 | ! ********* V(angle) = Ktheta(Theta - Theta0)**2 62 | ANGLES 63 | !! Alkane standard C27 parameeters. Not modified from original. 64 | HCA1A CC31A CC31A 34.500 110.10 22.53 2.179 ! alkane, 3/92 65 | HCA1A CC31A CC32A 34.500 110.10 22.53 2.179 ! alkane, 3/92 66 | HCA1A CC31A CC33A 34.500 110.10 22.53 2.179 ! alkane, 3/92 67 | HCA2A CC32A CC30A 26.500 110.10 22.53 2.179 ! alkane, 4/98 68 | HCA2A CC32A CC31A 26.500 110.10 22.53 2.179 ! alkane, 4/98 69 | HCA2A CC32A CC32A 26.500 110.10 22.53 2.179 ! alkane, 4/98 70 | HCA2A CC32A CC33A 34.600 110.10 22.53 2.179 ! alkane, 4/98 71 | HCA3A CC33A CC30A 33.430 110.10 22.53 2.179 ! alkane, 4/98 72 | HCA3A CC33A CC31A 33.430 110.10 22.53 2.179 ! alkane, 4/98 73 | HCA3A CC33A CC32A 34.600 110.10 22.53 2.179 ! alkane, 4/98 74 | HCA3A CC33A CC33A 37.500 110.10 22.53 2.179 ! alkane, 4/98 75 | HCA2A CC32A HCA2A 35.50 109.00 5.40 1.802 ! alkane, 3/92 76 | HCA3A CC33A HCA3A 35.50 108.40 5.40 1.802 ! alkane, 3/92 77 | CC30A CC32A CC32A 58.350 113.50 11.16 2.561 ! glycerol 78 | CC30A CC32A CC33A 58.350 113.50 11.16 2.561 ! glycerol 79 | CC31A CC31A CC31A 53.350 111.00 8.00 2.561 ! alkane, 3/92 80 | CC31A CC31A CC32A 58.350 113.50 11.16 2.561 ! glycerol 81 | CC31A CC31A CC33A 53.350 108.50 8.00 2.561 ! alkane, 3/92 82 | CC31A CC32A CC31A 58.350 113.50 11.16 2.561 ! glycerol 83 | CC31A CC32A CC32A 58.350 113.50 11.16 2.561 ! glycerol 84 | CC31A CC32A CC33A 58.350 113.50 11.16 2.561 ! glycerol 85 | CC32A CC30A CC32A 58.350 113.50 11.16 2.561 ! glycerol 86 | CC32A CC31A CC32A 58.350 113.50 11.16 2.561 ! glycerol 87 | CC32A CC32A CC32A 58.350 113.60 11.16 2.561 ! alkane, 3/92 88 | CC32A CC32A CC33A 58.000 115.00 8.00 2.561 ! alkane, 3/92 89 | CC33A CC30A CC33A 53.350 114.00 8.00 2.561 ! alkane 3/2/92 90 | CC33A CC31A CC32A 53.350 114.00 8.00 2.561 ! alkane 3/2/92 91 | CC33A CC31A CC33A 53.350 114.00 8.00 2.561 ! alkane 3/2/92 92 | CC33A CC32A CC33A 53.350 114.00 8.00 2.561 ! alkane 3/2/92 93 | !! 5-membered ring cyclopentane (cpen) ring parameters. viv modified Oct. 05 94 | CC325A CC325A CC325A 58.00 106.00 11.16 2.561 ! CPEN 10/17/05 viv 95 | HCA25A CC325A CC325A 35.00 111.40 22.53 2.179 ! CPEN 10/17/05 viv 96 | HCA25A CC325A HCA25A 38.50 106.80 5.40 1.802 ! CPEN 10/17/05 viv 97 | HCA25A CC325B CC325B 35.00 111.40 22.53 2.179 ! TF2M, viv 98 | HCA25A CC325B HCA25A 38.50 106.80 5.40 1.802 ! THF, 10/17/05 viv 99 | CC325B CC325B CC325B 58.00 109.50 11.16 2.561 ! THF, nucleotide CSD/NDB survey, 05/30/06, viv 100 | OC305A CC325B CC325B 45.00 111.10 ! THF 10/21/05, viv 101 | CC325B OC305A CC325B 95.00 111.00 ! THF 10/21/05, viv 102 | HCA25A CC325B OC305A 70.00 107.30 ! THF 10/21/05, viv 103 | HCA3A CC33A CC325B 34.600 110.10 22.53 2.179 ! TF2M viv 104 | CC325B CC325B CC33A 58.000 115.00 8.00 2.561 ! TF2M viv 105 | HCA25A CC325B CC33A 34.600 110.10 22.53 2.179 ! TF2M viv 106 | OC305A CC325B CC33A 45.00 111.50 ! TF2M, viv 107 | CC32A OC30A CC32A 95.00 109.70 ! DEET, diethylether, alex 108 | CC33A OC30A CC32A 95.00 109.70 ! DEET, diethylether, alex 109 | CC33A OC30A CC33A 95.00 109.70 ! DEET, diethylether, alex 110 | OC30A CC32A CC32A 45.00 111.50 ! DEET, diethylether, alex 111 | OC30A CC32A CC33A 45.00 111.50 ! DEET, diethylether, alex 112 | HCA3A CC33A OC30A 60.00 109.50 ! phosphate, alex 113 | HCA2A CC32A OC30A 60.00 109.50 ! phosphate, alex 114 | HCA2A CC326A CC326A 34.500 110.10 22.53 2.179 ! THP, sng cyclohexane 12/05 115 | HCA2A CC326A HCA2A 35.50 109.00 5.40 1.80200! THP, viv 116 | CC326A CC326A CC326A 58.350 112.00 11.16 2.561 ! THP, sng cyclohexane 12/05 117 | OC30A CC326A CC326A 45.00 111.50 ! THP, viv 118 | CC326A OC30A CC326A 95.00 109.70 ! THP, viv 119 | HCA2A CC326A OC30A 45.00 109.50 ! THP, sng 02/06 120 | 121 | ! ******** V(dihedral) = Kchi(1 + cos(n(chi) - delta)) 122 | DIHEDRALS 123 | !! Alkane standard C27 parameters. Not modified from original. 124 | CC31A CC30A CC32A HCA2A 0.20000 3 0.00 ! alkane, 3/92 125 | CC32A CC30A CC32A HCA2A 0.20000 3 0.00 ! alkane, 3/92 126 | CC33A CC30A CC32A HCA2A 0.20000 3 0.00 ! alkane, 3/92 127 | CC31A CC30A CC33A HCA3A 0.20000 3 0.00 ! alkane, 3/92 128 | CC32A CC30A CC32A HCA3A 0.20000 3 0.00 ! alkane, 3/92 129 | CC33A CC30A CC32A HCA3A 0.20000 3 0.00 ! alkane, 3/92 130 | HCA1A CC31A CC31A HCA1A 0.20000 3 0.00 ! alkane, 3/92 131 | CC31A CC31A CC31A HCA1A 0.20000 3 0.00 ! alkane, 3/92 132 | CC32A CC31A CC31A HCA1A 0.20000 3 0.00 ! alkane, 3/92 133 | CC33A CC31A CC31A HCA1A 0.20000 3 0.00 ! alkane, 3/92 134 | HCA1A CC31A CC32A HCA2A 0.20000 3 0.00 ! alkane, 3/92 135 | HCA1A CC31A CC32A CC31A 0.20000 3 0.00 ! alkane, 3/92 136 | HCA1A CC31A CC32A CC32A 0.20000 3 0.00 ! alkane, 3/92 137 | HCA1A CC31A CC32A CC33A 0.20000 3 0.00 ! alkane, 3/92 138 | CC31A CC31A CC32A HCA2A 0.20000 3 0.00 ! alkane, 3/92 139 | CC32A CC31A CC32A HCA2A 0.20000 3 0.00 ! alkane, 3/92 140 | CC33A CC31A CC32A HCA2A 0.20000 3 0.00 ! alkane, 3/92 141 | HCA1A CC31A CC33A HCA3A 0.20000 3 0.00 ! alkane, 3/92 142 | CC31A CC31A CC33A HCA3A 0.20000 3 0.00 ! alkane, 3/92 143 | CC32A CC31A CC33A HCA3A 0.20000 3 0.00 ! alkane, 3/92 144 | CC33A CC31A CC33A HCA3A 0.20000 3 0.00 ! alkane, 3/92 145 | HCA2A CC32A CC32A HCA2A 0.19000 3 0.0 ! alkane, 4/98, yin and mackerell 146 | CC30A CC32A CC32A HCA2A 0.19000 3 0.00 ! alkane, 4/98, yin and mackerell 147 | CC31A CC32A CC32A HCA2A 0.19000 3 0.00 ! alkane, 4/98, yin and mackerell 148 | CC32A CC32A CC32A HCA2A 0.19000 3 0.00 ! alkane, 4/98, yin and mackerell 149 | CC33A CC32A CC32A HCA2A 0.19000 3 0.00 ! alkane, 4/98, yin and mackerell 150 | HCA2A CC32A CC33A HCA3A 0.16000 3 0.0 ! alkane, 4/98, yin and mackerell 151 | CC30A CC32A CC33A HCA3A 0.16000 3 0.0 ! alkane, 4/98, yin and mackerell 152 | CC31A CC32A CC33A HCA3A 0.16000 3 0.0 ! alkane, 4/98, yin and mackerell 153 | CC32A CC32A CC33A HCA3A 0.16000 3 0.0 ! alkane, 4/98, yin and mackerell 154 | CC33A CC32A CC33A HCA3A 0.16000 3 0.0 ! alkane, 4/98, yin and mackerell 155 | CC33A CC32A CC32A CC33A 0.03179 6 180.0 ! alkane, c27r klauda et al 2004 156 | CC33A CC32A CC32A CC33A 0.03819 2 0.0 ! alkane, c27r klauda et al 2004 157 | CC33A CC32A CC32A CC32A 0.20391 5 0.0 ! alkane, c27r klauda et al 2004 158 | CC33A CC32A CC32A CC32A 0.10824 4 0.0 ! alkane, c27r klauda et al 2004 159 | CC33A CC32A CC32A CC32A 0.08133 3 180.0 ! alkane, c27r klauda et al 2004 160 | CC33A CC32A CC32A CC32A 0.15051 2 0.0 ! alkane, c27r klauda et al 2004 161 | CC32A CC32A CC32A CC32A 0.11251 5 0.0 ! alkane, c27r klauda et al 2004 162 | CC32A CC32A CC32A CC32A 0.09458 4 0.0 ! alkane, c27r klauda et al.2004 163 | CC32A CC32A CC32A CC32A 0.14975 3 180.0 ! alkane, c27r klauda et al 2004 164 | CC32A CC32A CC32A CC32A 0.06450 2 0.0 ! alkane, c27r klauda et al 2004 165 | CC33A CC325A CC325A CC33A 0.16000 3 0.0 !alkane, 4/98, yin and mackerell, cpen, viv 166 | CC33A CC325A CC325A CC325A 0.16000 3 0.0 !alkane, 4/98, yin and mackerell, cpen, viv 167 | CC33A CC325A CC325A HCA25A 0.16000 3 0.0 !alkane, 4/98, yin and mackerell, cpen, viv 168 | HCA25A CC325A CC325A HCA25A 0.16000 3 0.0 !alkane, 4/98, yin and mackerell, cpen, viv 169 | CC325A CC325A CC325A HCA25A 0.16000 3 0.0 !alkane, 4/98, yin and mackerell, cpen, viv 170 | CC325A CC325A CC325A CC325A 0.41000 3 180.0 ! cpen, cyclopentane, viv 10/4/05 171 | CC33A CC325B CC325B CC33A 0.19000 3 0.0 !alkane, 4/98, yin and mackerell, thf, viv 172 | CC33A CC325B CC325B CC325B 0.19000 3 0.0 !alkane, 4/98, yin and mackerell, thf, viv 173 | CC33A CC325B CC325B HCA25A 0.19000 3 0.0 !alkane, 4/98, yin and mackerell, thf, viv 174 | HCA25A CC325B CC325B HCA25A 0.19000 3 0.0 !alkane, 4/98, yin and mackerell, thf, viv 175 | CC325B CC325B CC325B HCA25A 0.19000 3 0.0 !alkane, 4/98, yin and mackerell, thf, viv 176 | OC305A CC325B CC325B HCA25A 0.19000 3 0.0 ! alkane, 4/98, yin and mackerell, thf viv 177 | HCA25A CC325B CC33A HCA3A 0.16000 3 0.0 ! alkane, 4/98, yin and mackerell, tf2m viv 178 | CC325B CC325B CC33A HCA3A 0.16000 3 0.0 ! alkane, 4/98, yin and mackerell, tf2m viv 179 | OC305A CC325B CC33A HCA3A 0.16000 3 0.0 ! alkane, 4/98, yin and mackerell, tf2m viv 180 | CC325B CC325B CC325B CC325B 0.41000 3 180.0 ! CPEN viv 10/4/05 181 | HCA25A CC325B OC305A CC325B 0.3000 3 0.0 ! THF, 05/30/06, viv 182 | OC305A CC325B CC325B CC325B 0.0000 3 0.0 ! THF, 05/30/06, viv 183 | CC325B CC325B OC305A CC325B 0.5000 3 0.0 ! THF, 05/30/06, viv 184 | CC33A CC325B OC305A CC325B 0.3000 3 0.0 ! THF, 05/30/06, viv 185 | CC33A CC326A CC326A CC33A 0.19000 3 0.0 !alkane, 4/98, yin and mackerell, thp, viv 186 | CC33A CC326A CC326A CC326A 0.19000 3 0.0 !alkane, 4/98, yin and mackerell, thp, viv 187 | CC33A CC326A CC326A HCA2A 0.19000 3 0.0 !alkane, 4/98, yin and mackerell, thp, viv 188 | HCA2A CC326A CC326A HCA2A 0.19000 3 0.0 !alkane, 4/98, yin and mackerell, thp, viv 189 | HCA2A CC326A CC326A CC326A 0.19000 3 0.0 !alkane, 4/98, yin and mackerell, thp, viv 190 | OC30A CC326A CC326A HCA2A 0.19000 3 0.0 !alkane, 4/98, yin and mackerell, thp viv 191 | HCA2A CC326A CC33A HCA3A 0.16000 3 0.0 ! alkane, 4/98, yin and mackerell, me-thp viv 192 | CC326A CC326A CC33A HCA3A 0.16000 3 0.0 ! alkane, 4/98, yin and mackerell, me-thp viv 193 | OC30A CC326A CC33A HCA3A 0.16000 3 0.0 ! alkane, 4/98, yin and mackerell, me-thp viv 194 | CC326A CC326A CC326A CC326A 0.49829 2 0.0 ! THP, viv 195 | CC326A CC326A CC326A CC326A -0.59844 3 0.0 ! THP, viv 196 | CC326A CC326A CC326A CC326A 0.41746 4 0.0 ! THP, viv 197 | CC326A CC326A CC326A CC326A -0.24829 5 0.0 ! THP, viv 198 | OC30A CC326A CC326A CC326A -0.19225 1 0.0 ! THP, sng 1/06 199 | OC30A CC326A CC326A CC326A -1.00000 2 0.0 ! THP, sng 1/06 200 | OC30A CC326A CC326A CC326A 0.59457 3 0.0 ! THP, sng 1/06 201 | OC30A CC326A CC326A CC326A -0.07862 4 0.0 ! THP, sng 1/06 202 | HCA3A CC33A CC33A HCA3A 0.15250 3 0.00 ! ETHA, ethane, 4/98, yin and mackerell 203 | CC326A OC30A CC326A CC326A -0.52702 1 0.0 ! THP, sng 1/06 204 | CC326A OC30A CC326A CC326A 0.68297 2 0.0 ! THP, sng 1/06 205 | CC326A OC30A CC326A CC326A -0.20977 3 0.0 ! THP, sng 1/06 206 | CC326A OC30A CC326A CC326A 0.15037 4 0.0 ! THP, sng 1/06 207 | CC326A OC30A CC326A HCA2A 0.28400 3 0.0 ! DMET, viv 208 | HCA2A CC32A CC32A OC30A 0.19000 3 0.0 ! alkane, 4/98, yin and mackerell 209 | OC30A CC32A CC33A HCA3A 0.16000 3 0.0 ! alkane, 4/98, yin and mackerell 210 | HCA2A CC32A OC30A CC32A 0.28400 3 0.0 ! DEET, diethylether, alex 211 | HCA3A CC33A OC30A CC32A 0.28400 3 0.0 ! DEET, diethylether, alex 212 | HCA2A CC32A OC30A CC33A 0.28400 3 0.0 ! DEET, diethylether, alex 213 | HCA3A CC33A OC30A CC33A 0.28400 3 0.0 ! DME, viv 214 | CC33A CC32A OC30A CC32A 0.40 1 0.0 ! diethylether, 2/12/05, ATM 215 | CC33A CC32A OC30A CC32A 0.49 3 0.0 ! diethylether 216 | CC33A CC32A OC30A CC33A 0.40 1 0.0 ! diethylether, 2/12/05, ATM, MEE viv 217 | CC33A CC32A OC30A CC33A 0.49 3 0.0 ! diethylether, MEE viv 218 | CC32A CC32A OC30A CC33A 0.57 1 0.0 ! 1,2 dimethoxyethane (DME), 2/12/05, ATM 219 | CC32A CC32A OC30A CC33A 0.29 2 0.0 ! 1,2 dimethoxyethane (DME) 220 | CC32A CC32A OC30A CC33A 0.43 3 0.0 ! 1,2 dimethoxyethane (DME) 221 | CC32A CC32A OC30A CC32A 0.57 1 0.0 ! 1,2 dimethoxyethane, 2/12/05, ATM 222 | CC32A CC32A OC30A CC32A 0.29 2 0.0 ! 1,2 dimethoxyethane 223 | CC32A CC32A OC30A CC32A 0.43 3 0.0 ! 1,2 dimethoxyethane 224 | OC30A CC32A CC32A OC30A 0.59 1 180.0 ! 1,2 dimethoxyethane, Aug 2007, HK Lee 225 | OC30A CC32A CC32A OC30A 1.16 2 0.0 ! 1,2 dimethoxyethane 226 | OC30A CC32A CC32A CC33A 0.16 1 180.0 ! methylpropylether, 2/12/05, ATM 227 | OC30A CC32A CC32A CC33A 0.39 2 0.0 ! methylpropylether 228 | OC30A CC32A CC32A CC32A 0.16 1 180.0 ! methylpropylether, 2/12/05, ATM 229 | OC30A CC32A CC32A CC32A 0.39 2 0.0 ! methylpropylether 230 | 231 | 232 | !********* V(Lennard-Jones) = Eps,i,j[(Rmin,i,j/ri,j)**12 - 2(Rmin,i,j/ri,j)**6] 233 | NONBONDED NBXMOD 5 ATOM CDIEL FSHIFT VATOM VDISTANCE VFSWITCH - 234 | CUTNB 14.0 CTOFNB 12.0 CTONNB 10.0 EPS 1.0 E14FAC 1.0 WMIN 1.5 235 | 236 | HCA1A 0.0 -0.0450 1.3400 ! alkane,isobutane 1/5/05 viv 237 | HCA2A 0.0 -0.0350 1.3400 ! alkane,propane 11/16/04 viv 238 | HCA3A 0.0 -0.0240 1.3400 ! alkane, yin and mackerell, 4/98 239 | !HT 0.0 -0.0460 0.2245 ! TIP3P water 240 | CC30A 0.0 -0.0320 2.0000 0.0 -0.01 1.9 ! from CC31A 241 | CC31A 0.0 -0.0320 2.0000 0.0 -0.01 1.9 ! alkane,isobutane 1/5/05 viv 242 | CC32A 0.0 -0.0560 2.0100 0.0 -0.01 1.9 ! alkane, 4/98, yin, adm jr. 243 | CC33A 0.0 -0.0780 2.0400 0.0 -0.01 1.9 ! alkane, 4/98, yin, adm jr. 244 | CC326A 0.0 -0.0560 2.0100 0.0 -0.01 1.9 ! THP, tetrahyropyran, viv 245 | HCA25A 0.0 -0.0350 1.3000 ! CPEN, cyclopentane, 8/06 viv 246 | CC325A 0.0 -0.0600 2.0200 0.0 -0.01 1.9 ! CPEN, cyclopentane, 8/06 viv 247 | CC325B 0.0 -0.0600 2.0200 0.0 -0.01 1.9 ! CPEN, cyclopentane, 8/06 viv 248 | OC305A 0.0 -0.1000 1.6500 ! THP, tetrahydropyran sng 1/06 249 | OC30A 0.0 -0.1000 1.6500 ! THP, tetrahydropyran sng 1/06 250 | 251 | END 252 | 253 | 254 | 255 | -------------------------------------------------------------------------------- /tma-aco/Common/charmm/par_all36_lipid.prm: -------------------------------------------------------------------------------- 1 | * \\\\\\\ CHARMM36 All-Hydrogen Lipid Parameter File /////// 2 | * All comments and questions should be submitted to the 3 | * parameter forum at the CHARMM website: www.charmm.org 4 | * 5 | 6 | !references 7 | ! 8 | !Jeffery B. Klauda, Richard M. Venable, J. Alfredo Freites, Joseph 9 | !W. O'Connor, Douglas J. Tobias, Carlos Mondragon-Ramirez, Igor 10 | !Vorobyov, Alexander D. MacKerell, Jr. and Richard W. Pastor "Update of 11 | !the CHARMM All-Atom Additive Force Field for Lipids: Validation on Six 12 | !Lipid Types" J. Phys. Chem. B 2010, 114, 7830-7843 13 | ! 14 | ! PUFA Modifications 15 | !Jeffery B. Klauda, Viviana Monje, Taehoon Kim, and Wonpil Im. "Improving 16 | !the CHARMM Force Field for Polyunsaturated Fatty Acid Chains" J. Phys. Chem. B. 17 | !2012 ASAP http://dx.doi.org/10.1021/jp304056p 18 | 19 | ATOMS 20 | MASS -1 HL 1.00800 ! polar H (equivalent to protein H) 21 | MASS -1 HCL 1.00800 ! charged H for PE (equivalent to protein HC) 22 | MASS -1 HOL 1.00800 ! Nucleic acid phosphate hydroxyl proton 23 | MASS -1 HAL1 1.00800 ! alphatic proton 24 | MASS -1 HAL2 1.00800 ! alphatic proton 25 | MASS -1 HAL3 1.00800 ! alphatic proton 26 | MASS -1 HEL1 1.00800 ! for alkene; RHC=CR 27 | MASS -1 HEL2 1.00800 ! for alkene; H2C=CR 28 | MASS -1 HBL 1.00800 ! POPS SER backbone H 29 | MASS -1 CL 12.01100 ! carbonyl C (acetic acid/methyl acetate) 30 | MASS -1 CTL1 12.01100 ! sp3 carbon with 1 H (-CH1-) 31 | MASS -1 CTL2 12.01100 ! carbon of methylene group (-CH2-) 32 | MASS -1 CTL3 12.01100 ! carbon of methyl group (-CH3) 33 | MASS -1 CTL5 12.01100 ! carbon of methyl group (-CH3) for tetramethylammonium 34 | MASS -1 CEL1 12.01100 ! for alkene; RHC=CR 35 | MASS -1 CEL2 12.01100 ! for alkene; H2C=CR 36 | MASS -1 CCL 12.01100 ! for POPS 37 | MASS -1 NTL 14.00700 ! ammonium nitrogen 38 | MASS -1 NH3L 14.00700 ! nitrogen phosphatidylethanolamine 39 | MASS -1 OBL 15.99940 ! acetic acid carboxyl oxygen (e. to protein OB) 40 | MASS -1 OCL 15.99940 ! acetate oxygen 41 | MASS -1 OSL 15.99940 ! ester oxygen 42 | MASS -1 O2L 15.99940 ! Nucleic acid =O in phosphate or sulfate 43 | MASS -1 OHL 15.99940 ! Nucleic acid phosphate hydroxyl oxygen 44 | MASS -1 OSLP 15.99940 ! Phosphate oxygen, to avoid conflict with methylacetate type O 45 | MASS -1 PL 30.97400 ! phosphorus 46 | MASS -1 SL 32.06000 ! Sulfate sulfur 47 | MASS -1 CRL1 12.01100 ! sp3 carbon with 1 H on a ring (-CH1-) for sterols 48 | MASS -1 CRL2 12.01100 ! carbon of methylene group on a ring (-CH2-) for sterols 49 | 50 | BONDS 51 | ! 52 | !V(bond) = Kb(b - b0)**2 53 | ! 54 | !Kb: kcal/mole/A**2 55 | !b0: A 56 | ! 57 | !atom type Kb b0 58 | ! 59 | CTL3 CL 200.0 1.522 ! methyl acetate 60 | CTL2 CL 200.0 1.522 ! methyl acetate 61 | CTL1 CL 200.0 1.522 ! methyl acetate 62 | CTL1 CCL 200.0 1.522 ! for POPS 63 | OBL CL 750.0 1.220 ! methyl acetate 64 | OCL CL 525.0 1.260 ! acetate, protein 65 | OCL CCL 525.0 1.260 ! for POPS 66 | OSL CL 150.0 1.334 ! methyl acetate 67 | OSLP CL 150.0 1.334 ! methyl acetate 68 | OHL CL 230.0 1.40 ! methyl acetate 69 | HOL OHL 545.0 0.960 ! acetic acid 70 | CTL1 HAL1 309.00 1.111 ! alkanes, 3/92 71 | CTL1 HBL 330.00 1.080 ! for POPS 72 | CTL2 HAL2 309.00 1.111 ! alkanes, 4/98 73 | CTL3 HAL3 322.00 1.111 ! alkanes, 4/98 74 | CTL3 OSL 340.0 1.43 ! phosphate 75 | CTL2 OSL 340.0 1.43 ! phosphate 76 | CTL1 OSL 340.0 1.43 ! phosphate 77 | CTL3 OSLP 340.0 1.43 ! 78 | CTL2 OSLP 340.0 1.43 ! 79 | CTL1 OSLP 340.0 1.43 ! 80 | OSL PL 270.0 1.60 ! phosphate 81 | OSLP PL 270.0 1.60 ! 82 | O2L PL 580.0 1.48 ! phosphate 83 | OHL PL 237.0 1.59 ! phosphate 84 | NH3L HCL 410.0 1.04 ! ethanolamine 85 | NH3L CTL1 200.0 1.48 ! for POPS 86 | NH3L CTL2 261.0 1.51 ! ethanolamine 87 | NTL CTL2 215.00 1.51 ! tetramethylammonium 88 | NTL CTL5 215.00 1.51 ! tetramethylammonium 89 | CTL5 HL 300.00 1.08 ! tetramethylammonium 90 | CTL2 HL 300.00 1.08 ! tetramethylammonium 91 | CTL1 CTL1 222.500 1.500 ! alkanes, 3/92 92 | CTL1 CTL2 222.500 1.538 ! alkanes, 3/92 93 | CTL1 CTL3 222.500 1.538 ! alkanes, 3/92 94 | CTL2 CTL2 222.500 1.530 ! alkanes, 3/92 95 | CTL2 CTL3 222.500 1.528 ! alkanes, 3/92 96 | CTL3 CTL3 222.500 1.530 ! alkanes, 3/92 97 | OHL CTL1 428.0 1.420 ! glycerol 98 | OHL CTL2 428.0 1.420 ! glycerol 99 | OHL CTL3 428.0 1.420 ! glycerol 100 | SL O2L 540.0 1.448 ! methylsulfate 101 | SL OSL 250.0 1.575 ! methylsulfate 102 | CEL2 CEL2 510.000 1.330 ! ethene yin,adm jr., 12/95 103 | HEL2 CEL2 365.000 1.100 ! propene; from ethene, yin,adm jr., 12/95 104 | CEL1 CTL3 383.000 1.504 ! butene, yin,adm jr., 12/95 105 | CEL1 CEL2 500.000 1.342 ! propene, yin,adm jr., 12/95 106 | HEL1 CEL1 360.500 1.100 ! propene, yin,adm jr., 12/95 107 | CEL1 CTL2 365.000 1.502 ! butene; from propene, yin,adm jr., 12/95 108 | CEL1 CEL1 440.000 1.340 ! butene, yin,adm jr., 12/95 109 | 110 | ANGLES 111 | ! 112 | !V(angle) = Ktheta(Theta - Theta0)**2 113 | ! 114 | !V(Urey-Bradley) = Kub(S - S0)**2 115 | ! 116 | !Ktheta: kcal/mole/rad**2 117 | !Theta0: degrees 118 | !Kub: kcal/mole/A**2 (Urey-Bradley) 119 | !S0: A 120 | ! 121 | !atom types Ktheta Theta0 Kub S0 122 | ! 123 | ! 124 | OBL CL CTL3 70.0 125.0 20.0 2.442 ! methyl acetate 125 | OBL CL CTL2 70.0 125.0 20.0 2.442 ! methyl acetate 126 | OBL CL CTL1 70.0 125.0 20.0 2.442 ! methyl acetate 127 | OSL CL OBL 90.0 125.9 160.0 2.2576 ! acetic acid 128 | CL OSL CTL1 40.0 109.6 30.0 2.2651 ! methyl acetate 129 | CL OSL CTL2 40.0 109.6 30.0 2.2651 ! methyl acetate 130 | CL OSL CTL3 40.0 109.6 30.0 2.2651 ! methyl acetate 131 | HAL2 CTL2 CL 33.00 109.50 30.00 2.163 ! methyl acetate 132 | HAL3 CTL3 CL 33.00 109.50 30.00 2.163 ! methyl acetate 133 | CTL2 CTL2 CL 52.0 108.00 ! alkane 134 | CTL2 CTL1 CCL 52.0 108.00 ! for POPS 135 | CTL3 CTL2 CL 52.0 108.00 ! alkane 136 | OSL CL CTL3 55.0 109.0 20.00 2.3260 ! methyl acetate 137 | OSL CL CTL2 55.0 109.0 20.00 2.3260 ! methyl acetate 138 | OSL CL CTL1 55.0 109.0 20.00 2.3260 ! methyl acetate 139 | OHL CL OBL 50.0 123.0 210.0 2.2620 ! acetic acid 140 | OCL CL CTL2 40.0 118.0 50.0 2.3880 ! acetate 141 | OCL CL CTL3 40.0 118.0 50.0 2.3880 ! acetate 142 | OCL CL OCL 100.0 124.0 70.0 2.2250 ! acetate 143 | OCL CCL OCL 100.0 124.0 70.0 2.2250 ! for POPS 144 | OCL CCL CTL1 40.0 118.0 50.0 2.3880 ! for POPS 145 | OHL CL CTL3 55.0 110.50 ! acetic acid 146 | OHL CL CTL2 55.0 110.50 ! acetic acid 147 | HOL OHL CL 55.0 115.0 ! acetic acid 148 | OSL CTL1 CTL1 75.700 110.10 ! acetic acid, PIP 149 | OSL CTL1 CTL2 75.700 110.10 ! acetic acid 150 | OSL CTL1 CTL3 75.700 110.10 ! acetic acid 151 | OSL CTL2 CTL1 75.700 110.10 ! acetic acid 152 | OSL CTL2 CTL2 75.700 110.10 ! acetic acid 153 | OSL CTL2 CTL3 75.700 110.10 ! acetic acid 154 | OSLP CTL1 CTL1 75.700 110.10 ! acetic acid, PIP 155 | OSLP CTL1 CTL2 75.700 110.10 ! acetic acid 156 | OSLP CTL1 CTL3 75.700 110.10 ! acetic acid 157 | OSLP CTL2 CTL1 75.700 110.10 ! acetic acid 158 | OSLP CTL2 CTL2 75.700 110.10 ! acetic acid 159 | OSLP CTL2 CTL3 75.700 110.10 ! acetic acid 160 | HAL2 CTL2 HAL2 35.500 109.00 5.40 1.80200 ! alkane, 3/92 161 | HAL3 CTL3 HAL3 35.500 108.40 5.40 1.80200 ! alkane, 3/92 162 | HAL1 CTL1 OSL 60.0 109.5 ! phosphate 163 | HAL2 CTL2 OSL 60.0 109.5 ! phosphate 164 | HAL3 CTL3 OSL 60.0 109.5 ! phosphate 165 | HAL1 CTL1 OSLP 60.0 109.5 ! phosphate 166 | HAL2 CTL2 OSLP 60.0 109.5 ! phosphate 167 | HAL3 CTL3 OSLP 60.0 109.5 ! phosphate 168 | CTL1 OSL PL 20.0 120.0 35.0 2.33 ! phosphate, PIP 169 | CTL2 OSL PL 20.0 120.0 35.0 2.33 ! phosphate 170 | CTL3 OSL PL 20.0 120.0 35.0 2.33 ! phosphate 171 | CTL1 OSLP PL 20.0 120.0 35.0 2.33 ! phosphate, PIP 172 | CTL2 OSLP PL 20.0 120.0 35.0 2.33 ! phosphate 173 | CTL3 OSLP PL 20.0 120.0 35.0 2.33 ! phosphate 174 | HOL OHL PL 30.0 115.0 40.0 2.30 ! phosphate 175 | OSL PL OSL 80.0 104.3 ! phosphate 176 | OSL PL O2L 98.9 111.6 ! phosphate 177 | OSL PL OHL 48.1 108.0 ! phosphate 178 | OSLP PL OSLP 80.0 104.3 ! phosphate 179 | OSLP PL O2L 98.9 111.6 ! phosphate 180 | OSLP PL OHL 48.1 108.0 ! phosphate 181 | O2L PL O2L 120.0 120.0 ! phosphate 182 | O2L PL OHL 98.9 108.23 ! phosphate 183 | NTL CTL2 HL 40.0 109.5 27. 2.13 ! tetramethylammonium 184 | NTL CTL5 HL 40.0 109.5 27. 2.13 ! tetramethylammonium 185 | HL CTL2 HL 24.0 109.50 28. 1.767 ! tetramethylammonium 186 | HL CTL5 HL 24.0 109.50 28. 1.767 ! tetramethylammonium 187 | CTL2 NTL CTL2 60.0 109.5 26. 2.466 ! tetraethylammonium, from CTL5 NTL CTL2 188 | CTL5 NTL CTL2 60.0 109.5 26. 2.466 ! tetramethylammonium 189 | CTL5 NTL CTL5 60.0 109.5 26. 2.466 ! tetramethylammonium 190 | HL CTL2 CTL2 33.430 110.10 22.53 2.179 ! alkane 191 | HL CTL2 CTL3 33.430 110.10 22.53 2.179 ! alkane 192 | HAL1 CTL1 CTL1 34.500 110.10 22.53 2.179 ! alkane, 3/92 193 | HAL1 CTL1 CTL2 34.500 110.10 22.53 2.179 ! alkane, 3/92 194 | HAL1 CTL1 CTL3 34.500 110.10 22.53 2.179 ! alkane, 3/92 195 | HAL2 CTL2 CTL1 26.500 110.10 22.53 2.179 ! alkane, 4/98 196 | HAL2 CTL2 CTL2 26.500 110.10 22.53 2.179 ! alkane, 4/98 197 | HAL2 CTL2 CTL3 34.600 110.10 22.53 2.179 ! alkane, 4/98 198 | HAL3 CTL3 CTL1 33.430 110.10 22.53 2.179 ! alkane, 4/98 199 | HAL3 CTL3 CTL2 34.600 110.10 22.53 2.179 ! alkane, 4/98 200 | HAL3 CTL3 CTL3 37.500 110.10 22.53 2.179 ! alkane, 4/98 201 | HBL CTL1 CCL 50.000 109.50 ! for POPS 202 | HBL CTL1 CTL2 35.000 111.00 ! for POPS 203 | NTL CTL2 CTL2 67.7 115.00 ! tetramethylammonium 204 | NTL CTL2 CTL3 67.7 115.00 ! tetramethylammonium 205 | HCL NH3L CTL2 33.0 109.50 4.00 2.056 ! ethanolamine 206 | HCL NH3L CTL1 30.0 109.50 20.00 2.074 ! for POPS 207 | HCL NH3L HCL 41.0 109.50 ! ethanolamine 208 | NH3L CTL2 CTL2 67.7 110.00 ! ethanolamine 209 | NH3L CTL2 HAL2 45.0 107.50 35.00 2.0836 ! ethanolamine 210 | CTL1 CTL1 CTL1 53.350 111.00 8.00 2.561 ! alkane, 3/92 211 | NH3L CTL1 CCL 43.7 110.00 ! for POPS 212 | NH3L CTL1 CTL2 67.7 110.00 ! for POPS 213 | NH3L CTL1 HBL 51.5 107.50 ! for POPS 214 | CTL1 CTL1 CTL2 58.350 113.50 11.16 2.561 ! glycerol 215 | CTL1 CTL1 CTL3 53.350 108.50 8.00 2.561 ! alkane, 3/92 216 | CTL1 CTL2 CTL1 58.350 113.50 11.16 2.561 ! glycerol 217 | CTL1 CTL2 CTL2 58.350 113.50 11.16 2.561 ! glycerol 218 | CTL1 CTL2 CTL3 58.350 113.50 11.16 2.561 ! glycerol 219 | CTL2 CTL1 CTL2 58.350 113.50 11.16 2.561 ! glycerol 220 | CTL2 CTL1 CTL3 58.350 113.50 11.16 2.561 ! glycerol 221 | CTL2 CTL2 CTL2 58.350 113.60 11.16 2.561 ! alkane, 3/92 222 | CTL2 CTL2 CTL3 58.000 115.00 8.00 2.561 ! alkane, 3/92 223 | CTL3 CTL1 CTL3 58.350 113.50 11.16 2.561 ! glycerol 224 | HOL OHL CTL1 57.500 106.00 ! glycerol 225 | HOL OHL CTL2 57.500 106.00 ! glycerol 226 | HOL OHL CTL3 57.500 106.00 ! glycerol 227 | OHL CTL1 CTL1 75.700 110.10 ! glycerol, PIP 228 | OHL CTL1 CTL2 75.700 110.10 ! glycerol 229 | OHL CTL2 CTL1 75.700 110.10 ! glycerol 230 | OHL CTL2 CTL2 75.700 110.10 ! glycerol 231 | OHL CTL2 CTL3 75.700 110.10 ! glycerol 232 | OHL CTL1 HAL1 45.900 108.89 ! glycerol 233 | OHL CTL2 HAL2 45.900 108.89 ! glycerol 234 | OHL CTL3 HAL3 45.900 108.89 ! glycerol 235 | O2L SL O2L 130.0 109.47 35.0 2.45 ! methylsulfate 236 | O2L SL OSL 85.0 98.0 ! methylsulfate 237 | CTL2 OSL SL 15.0 109.0 27.00 1.90 ! methylsulfate 238 | CTL3 OSL SL 15.0 109.0 27.00 1.90 ! methylsulfate 239 | CEL1 CEL1 CTL2 48.00 123.50 ! from 2-butene, yin,adm jr., 12/95 240 | CEL1 CEL1 CTL3 48.00 123.50 ! 2-butene, yin,adm jr., 12/95 241 | CEL2 CEL1 CTL2 48.00 126.00 ! 1-butene; from propene, yin,adm jr., 12/95 242 | CEL2 CEL1 CTL3 47.00 125.20 ! propene, yin,adm jr., 12/95 243 | HEL1 CEL1 CEL1 52.00 119.50 ! 2-butene, yin,adm jr., 12/95 244 | HEL1 CEL1 CEL2 42.00 118.00 ! propene, yin,adm jr., 12/95 245 | HEL1 CEL1 CTL2 40.00 116.00 ! 1-butene; from propene, yin,adm jr., 12/95 246 | HEL1 CEL1 CTL3 22.00 117.00 ! propene, yin,adm jr., 12/95 247 | HEL2 CEL2 CEL1 45.00 120.50 ! propene, yin,adm jr., 12/95 248 | HEL2 CEL2 CEL2 55.50 120.50 ! ethene, yin,adm jr., 12/95 249 | HEL2 CEL2 HEL2 19.00 119.00 ! propene, yin,adm jr., 12/95 250 | CEL1 CTL2 CTL2 32.00 112.20 ! 1-butene; from propene, yin,adm jr., 12/95 251 | CEL1 CTL2 CTL3 32.00 112.20 ! 1-butene; from propene, yin,adm jr., 12/95 252 | HAL2 CTL2 CEL1 45.00 111.50 ! 1-butene; from propene, yin,adm jr., 12/95 253 | HAL3 CTL3 CEL1 42.00 111.50 ! 2-butene, yin,adm jr., 12/95 254 | CEL1 CTL2 CEL1 30.0 114.0 ! 1,4-dipentene, adm jr., 2/00 255 | 256 | DIHEDRALS 257 | ! 258 | !V(dihedral) = Kchi(1 + cos(n(chi) - delta)) 259 | ! 260 | !Kchi: kcal/mole 261 | !n: multiplicity 262 | !delta: degrees 263 | ! 264 | !atom types Kchi n delta 265 | ! 266 | X CTL1 OHL X 0.14 3 0.00 ! glycerol 267 | X CTL2 OHL X 0.14 3 0.00 ! glycerol 268 | X CTL3 OHL X 0.14 3 0.00 ! glycerol 269 | OCL CCL CTL1 NH3L 3.20 2 180.00 ! for POPS 270 | OBL CL CTL2 HAL2 0.00 6 180.00 ! acetic acid 271 | OBL CL CTL3 HAL3 0.00 6 180.00 ! acetic acid 272 | OSL CL CTL2 HAL2 0.00 6 180.00 ! acetic acid 273 | OSL CL CTL3 HAL3 0.00 6 180.00 ! acetic acid 274 | OSLP CL CTL2 HAL2 0.00 6 180.00 ! acetic acid 275 | OSLP CL CTL3 HAL3 0.00 6 180.00 ! acetic acid 276 | OBL CL OSL CTL1 0.965 1 180.00 ! methyl acetate 277 | OBL CL OSL CTL1 3.85 2 180.00 ! methyl acetate 278 | OBL CL OSL CTL2 0.965 1 180.00 ! methyl acetate 279 | OBL CL OSL CTL2 3.85 2 180.00 ! methyl acetate 280 | OBL CL OSL CTL3 0.965 1 180.00 ! methyl acetate 281 | OBL CL OSL CTL3 3.85 2 180.00 ! methyl acetate 282 | X CL OSL X 2.05 2 180.00 ! methyl acetate 283 | X CTL2 CL X 0.05 6 180.00 ! methyl acetate 284 | X CTL3 CL X 0.05 6 180.00 ! methyl acetate 285 | X CL OHL X 2.05 2 180.00 ! acetic acid 286 | X CTL1 CCL X 0.05 6 180.00 ! for POPS 287 | HAL2 CTL2 CL OHL 0.00 6 180.00 288 | HAL3 CTL3 CL OHL 0.00 6 180.00 289 | PL OSLP CTL2 CTL1 0.407 2 0.00 ! Phos-gly, 8/05 290 | PL OSLP CTL2 CTL1 0.241 1 180.00 ! Phos-gly, 8/05 291 | PL OSLP CTL2 CTL2 0.407 2 0.00 ! Phos-gly, 8/05 292 | PL OSLP CTL2 CTL2 0.241 1 180.00 ! Phos-gly, 8/05 293 | OSL PL OSL CTL1 1.20 1 180.00 ! phosphate, new NA, 4/98, adm jr., PIP 294 | OSL PL OSL CTL1 0.10 2 180.00 ! phosphate, new NA, 4/98, adm jr., PIP 295 | OSL PL OSL CTL1 0.10 3 180.00 ! phosphate, new NA, 4/98, adm jr., PIP 296 | OSLP PL OSLP CTL1 1.20 1 180.00 ! phosphate, new NA, 4/98, adm jr., PIP 297 | OSLP PL OSLP CTL1 0.10 2 180.00 ! phosphate, new NA, 4/98, adm jr., PIP 298 | OSLP PL OSLP CTL1 0.10 3 180.00 ! phosphate, new NA, 4/98, adm jr., PIP 299 | OSLP PL OSLP CTL2 1.20 1 180.00 ! phosphate, new NA, 4/98, adm jr. 300 | OSLP PL OSLP CTL2 0.10 2 180.00 ! phosphate, new NA, 4/98, adm jr. 301 | OSLP PL OSLP CTL2 0.10 3 180.00 ! phosphate, new NA, 4/98, adm jr. 302 | O2L PL OSLP CTL2 0.10 3 0.00 ! phosphate, new NA, 4/98, adm jr. 303 | O2L PL OSL CTL2 0.10 3 0.00 ! phosphate, new NA, 4/98, adm jr. 304 | OSLP PL OSLP CTL3 1.20 1 180.00 ! phosphate, new NA, 4/98, adm jr. 305 | OSLP PL OSLP CTL3 0.10 2 180.00 ! phosphate, new NA, 4/98, adm jr. 306 | OSLP PL OSLP CTL3 0.10 3 180.00 ! phosphate, new NA, 4/98, adm jr. 307 | O2L PL OSLP CTL1 0.10 3 0.00 ! phosphate, new NA, 4/98, adm jr., PIP 308 | O2L PL OSL CTL1 0.10 3 0.00 ! phosphate, new NA, 4/98, adm jr., PIP 309 | O2L PL OSLP CTL3 0.10 3 0.00 ! phosphate, new NA, 4/98, adm jr. 310 | O2L PL OSL CTL3 0.10 3 0.00 ! phosphate, new NA, 4/98, adm jr. 311 | OHL PL OSL CTL1 0.95 2 0.00 ! terminal phosphate, PIP 312 | OHL PL OSL CTL1 0.50 3 0.00 ! terminal phosphate, PIP 313 | OHL PL OSL CTL2 0.95 2 0.00 ! terminal phosphate 314 | OHL PL OSL CTL2 0.50 3 0.00 ! terminal phosphate 315 | OHL PL OSL CTL3 0.95 2 0.00 ! terminal phosphate 316 | OHL PL OSL CTL3 0.50 3 0.00 ! terminal phosphate 317 | OHL PL OSLP CTL2 0.95 2 0.00 ! terminal phosphate 318 | OHL PL OSLP CTL2 0.50 3 0.00 ! terminal phosphate 319 | OHL PL OSLP CTL3 0.95 2 0.00 ! terminal phosphate 320 | OHL PL OSLP CTL3 0.50 3 0.00 ! terminal phosphate 321 | X OHL PL X 0.30 3 0.00 ! terminal phosphate 322 | X CTL1 OSL X 0.00 3 0.00 ! phosphate, new NA, 4/98, adm jr. 323 | X CTL2 OSL X 0.00 3 0.00 ! phosphate, new NA, 4/98, adm jr. 324 | X CTL3 OSL X 0.00 3 0.00 ! phosphate, new NA, 4/98, adm jr. 325 | X CTL1 OSLP X 0.00 3 0.00 ! phosphate, new NA, 4/98, adm jr. 326 | X CTL2 OSLP X 0.00 3 0.00 ! phosphate, new NA, 4/98, adm jr. 327 | X CTL3 OSLP X 0.00 3 0.00 ! phosphate, new NA, 4/98, adm jr. 328 | CTL1 CTL2 CL OSL -0.15 1 180.00 ! methyl propionate, 12/92 329 | CTL1 CTL2 CL OSL 0.53 2 180.00 ! methyl propionate, 12/92 330 | CTL2 CTL2 CL OSL 0.000 6 0.00 ! glycerol & propl ester, 6/07 331 | CTL2 CTL2 CL OSL 0.030 3 180.00 ! glycerol & propl ester, 6/07 332 | CTL2 CTL2 CL OSL 0.432 2 180.00 ! glycerol & propl ester, 6/07 333 | CTL2 CTL2 CL OSL 0.332 1 0.00 ! glycerol & propl ester, 6/07 334 | CTL3 CTL2 CL OSL 0.000 6 0.00 ! glycerol & propl ester, 6/07 335 | CTL3 CTL2 CL OSL 0.030 3 180.00 ! glycerol & propl ester, 6/07 336 | CTL3 CTL2 CL OSL 0.432 2 180.00 ! glycerol & propl ester, 6/07 337 | CTL3 CTL2 CL OSL 0.332 1 0.00 ! glycerol & propl ester, 6/07 338 | CTL3 CTL2 CTL2 CL 0.000 5 180.00 ! propyl ester, 6/07 339 | CTL3 CTL2 CTL2 CL 0.317 3 180.00 ! propyl ester, 6/07 340 | CTL3 CTL2 CTL2 CL 0.557 2 0.00 ! propyl ester, 6/07 341 | CTL3 CTL2 CTL2 CL 0.753 1 0.00 ! propyl ester, 6/07 342 | CTL2 CTL2 CTL2 CL 0.000 5 180.00 ! propyl ester, 6/07 343 | CTL2 CTL2 CTL2 CL 0.317 3 180.00 ! propyl ester, 6/07 344 | CTL2 CTL2 CTL2 CL 0.557 2 0.00 ! propyl ester, 6/07 345 | CTL2 CTL2 CTL2 CL 0.753 1 0.00 ! propyl ester, 6/07 346 | OSL CTL2 CTL1 OSL -0.429 4 60.00 ! glycerol, 8/08 347 | OSL CTL2 CTL1 OSL 0.614 3 0.00 ! glycerol, 8/08 348 | OSL CTL2 CTL1 OSL -0.115 2 60.00 ! glycerol, 8/08 349 | OSL CTL2 CTL1 OSL 0.703 1 180.00 ! glycerol, 8/08 350 | OSLP CTL2 CTL1 OSL 0.000 4 0.00 ! Fit to QM, theta2, 07/08 jbk 351 | OSLP CTL2 CTL1 OSL 0.607 3 180.00 ! Fit to QM, theta2, 07/08 jbk 352 | OSLP CTL2 CTL1 OSL 0.254 2 60.00 ! Fit to QM, theta2, 07/08 jbk 353 | OSLP CTL2 CTL1 OSL 2.016 1 180.00 ! Fit to QM, theta2, 07/08 jbk 354 | OSLP CTL2 CTL2 OSL 0.000 4 0.00 ! Fit to QM, theta2, 07/08 jbk 355 | OSLP CTL2 CTL2 OSL 0.607 3 180.00 ! Fit to QM, theta2, 07/08 jbk 356 | OSLP CTL2 CTL2 OSL 0.254 2 60.00 ! Fit to QM, theta2, 07/08 jbk 357 | OSLP CTL2 CTL2 OSL 2.016 1 180.00 ! Fit to QM, theta2, 07/08 jbk 358 | CTL3 CTL1 CTL2 OSL 0.000 3 0.00 ! glycerol, theta3 359 | CTL2 CTL1 CTL2 OSL 0.000 3 0.00 ! glycerol, theta3 360 | CTL3 CTL2 CTL2 OSL 0.000 3 0.00 ! glycerol, theta3 361 | CTL2 CTL2 CTL2 OSL 0.000 3 0.00 ! glycerol, theta3 362 | CL OSL CTL1 CTL2 0.000 4 0.00 ! glycerol, beta1 6/07 363 | CL OSL CTL1 CTL2 0.150 3 180.00 ! glycerol, beta1 6/07 364 | CL OSL CTL1 CTL2 1.453 2 180.00 ! glycerol, beta1 6/07 365 | CL OSL CTL1 CTL2 0.837 1 180.00 ! glycerol, beta1 6/07 366 | CL OSL CTL1 CTL3 0.000 4 0.00 ! glycerol, beta1 6/07 367 | CL OSL CTL1 CTL3 0.150 3 180.00 ! glycerol, beta1 6/07 368 | CL OSL CTL1 CTL3 1.453 2 180.00 ! glycerol, beta1 6/07 369 | CL OSL CTL1 CTL3 0.837 1 180.00 ! glycerol, beta1 6/07 370 | CL OSL CTL2 CTL1 0.267 3 180.00 ! glycerol, gamma1 6/07 371 | CL OSL CTL2 CTL1 0.173 2 0.00 ! glycerol, gamma1 6/07 372 | CL OSL CTL2 CTL1 0.781 1 180.00 ! glycerol, gamma1 6/07 373 | X CTL2 NTL X 0.26 3 0.00 ! tetramethylammonium 374 | X CTL5 NTL X 0.23 3 0.00 ! tetramethylammonium 375 | X CTL1 NH3L X 0.10 3 0.00 ! for POPS 376 | X CTL2 NH3L X 0.10 3 0.00 ! ethanolamine 377 | NH3L CTL2 CTL2 OHL 0.7 1 180.00 ! ethanolamine 378 | NH3L CTL2 CTL2 OSLP 0.7 1 180.00 ! ethanolamine 379 | NTL CTL2 CTL2 OHL 4.3 1 180.00 ! choline, 12/92 380 | NTL CTL2 CTL2 OHL -0.4 3 180.00 ! choline, 12/92 381 | NTL CTL2 CTL2 OSLP 3.3 1 180.00 ! choline, 12/92 382 | NTL CTL2 CTL2 OSLP -0.4 3 180.00 ! choline, 12/92 383 | X CTL1 CTL1 X 0.200 3 0.00 ! alkane, 3/92 384 | X CTL1 CTL2 X 0.200 3 0.00 ! alkane, 3/92 385 | X CTL1 CTL3 X 0.200 3 0.00 ! alkane, 3/92 386 | X CTL2 CTL2 X 0.1900 3 0.00 ! alkane, 4/98, yin and mackerell 387 | X CTL2 CTL3 X 0.1600 3 0.00 ! alkane, 4/98, yin and mackerell 388 | X CTL3 CTL3 X 0.1525 3 0.00 ! alkane, 4/98, yin and mackerell 389 | !alkane CCCC dihedrals based on pentane, heptane and hexane vdz/vqz/ccsd(t) QM data 390 | CTL3 CTL2 CTL2 CTL3 0.060 2 0.00 ! alkane, 7/08, jbk 391 | CTL3 CTL2 CTL2 CTL3 0.035 5 0.00 ! alkane, 7/08, jbk 392 | CTL2 CTL2 CTL2 CTL3 0.162 2 0.00 ! alkane, 7/08, jbk 393 | CTL2 CTL2 CTL2 CTL3 0.047 3 180.00 ! alkane, 7/08, jbk 394 | CTL2 CTL2 CTL2 CTL3 0.105 4 0.00 ! alkane, 7/08, jbk 395 | CTL2 CTL2 CTL2 CTL3 0.177 5 0.00 ! alkane, 7/08, jbk 396 | CTL2 CTL2 CTL2 CTL2 0.101 2 0.00 ! alkane, 7/08, jbk 397 | CTL2 CTL2 CTL2 CTL2 0.142 3 180.00 ! alkane, 7/08, jbk 398 | CTL2 CTL2 CTL2 CTL2 0.074 4 0.00 ! alkane, 7/08, jbk 399 | CTL2 CTL2 CTL2 CTL2 0.097 5 0.00 ! alkane, 7/08, jbk 400 | HAL3 CTL3 OSL SL 0.00 3 0.00 ! methylsulfate 401 | CTL2 OSL SL O2L 0.00 3 0.00 ! methylsulfate 402 | CTL3 OSL SL O2L 0.00 3 0.00 ! methylsulfate 403 | HEL1 CEL1 CEL1 HEL1 1.0000 2 180.00 ! 2-butene, adm jr., 8/98 update 404 | CTL3 CEL1 CEL1 HEL1 1.0000 2 180.00 ! 2-butene, adm jr., 8/98 update 405 | X CEL1 CEL1 X 0.4500 1 180.00 ! 2-butene, adm jr., 4/04 406 | X CEL1 CEL1 X 8.5000 2 180.00 ! 407 | X CEL2 CEL2 X 4.9000 2 180.00 ! ethene, yin,adm jr., 12/95 408 | CTL2 CEL1 CEL2 HEL2 5.2000 2 180.00 ! propene, yin,adm jr., 12/95 409 | CTL3 CEL1 CEL2 HEL2 5.2000 2 180.00 ! propene, yin,adm jr., 12/95 410 | HEL1 CEL1 CEL2 HEL2 5.2000 2 180.00 ! propene, yin,adm jr., 12/95 411 | !alkene update, 2004,2009 412 | CEL1 CEL1 CTL2 HAL2 0.3000 3 180.00 !2-butene, adm jr., 4/04 413 | CEL1 CEL1 CTL3 HAL3 0.3000 3 180.00 !2-butene, adm jr., 4/04 414 | !CEL1 CEL1 CTL2 CTL3 0.9000 1 180.00 !2-pentene and 3-heptene 415 | !CEL1 CEL1 CTL2 CTL3 0.2000 2 180.00 !2-pentene and 3-heptene 416 | CEL1 CEL1 CTL2 CTL3 0.9100 1 180.0 !2-hexene, adm jr., 11/09, end fix jbk 417 | CEL1 CEL1 CTL2 CTL3 0.1800 2 180.0 !2-hexene, adm jr., 11/09 418 | CEL1 CEL1 CTL2 CTL3 0.1700 3 180.0 !2-hexene, adm jr., 11/09 419 | CEL1 CEL1 CTL2 CTL2 0.9100 1 180.0 !2-hexene, adm jr., 11/09 420 | CEL1 CEL1 CTL2 CTL2 0.1800 2 180.0 !2-hexene, adm jr., 11/09 421 | CEL1 CEL1 CTL2 CTL2 0.1700 3 180.0 !2-hexene, adm jr., 11/09 422 | CEL1 CTL2 CTL2 CL 0.1400 1 180.0 !2-hexene, adm jr., 11/09, add jbk for DHA 423 | CEL1 CTL2 CTL2 CL 0.1700 2 0.0 !2-hexene, adm jr., 11/09, add jbk for DHA 424 | CEL1 CTL2 CTL2 CL 0.0500 3 180.0 !2-hexene, adm jr., 11/09, add jbk for DHA 425 | CEL1 CTL2 CTL2 CTL2 0.1400 1 180.0 !2-hexene, adm jr., 11/09 426 | CEL1 CTL2 CTL2 CTL2 0.1700 2 0.0 !2-hexene, adm jr., 11/09 427 | CEL1 CTL2 CTL2 CTL2 0.0500 3 180.0 !2-hexene, adm jr., 11/09 428 | CEL1 CTL2 CTL2 CTL3 0.1400 1 180.0 !2-hexene, adm jr., 11/09 429 | CEL1 CTL2 CTL2 CTL3 0.1700 2 0.0 !2-hexene, adm jr., 11/09 430 | CEL1 CTL2 CTL2 CTL3 0.0500 3 180.0 !2-hexene, adm jr., 11/09 431 | CEL2 CEL1 CTL2 CTL2 0.5000 1 180.00 ! 1-butene, adm jr., 2/00 update 432 | CEL2 CEL1 CTL2 CTL2 1.3000 3 180.00 ! 1-butene, adm jr., 2/00 update 433 | CEL2 CEL1 CTL2 CTL3 0.5000 1 180.00 ! 1-butene, adm jr., 2/00 update 434 | CEL2 CEL1 CTL2 CTL3 1.3000 3 180.00 ! 1-butene, adm jr., 2/00 update 435 | CEL2 CEL1 CTL2 HAL2 0.1200 3 0.00 ! 1-butene, yin,adm jr., 12/95 436 | CEL2 CEL1 CTL3 HAL3 0.0500 3 180.00 ! propene, yin,adm jr., 12/95 437 | HEL1 CEL1 CTL2 CTL2 0.1200 3 0.00 ! butene, yin,adm jr., 12/95 438 | HEL1 CEL1 CTL2 CTL3 0.1200 3 0.00 ! butene, yin,adm jr., 12/95 439 | HEL1 CEL1 CTL2 HAL2 0.0000 3 0.00 ! butene, adm jr., 2/00 update 440 | HEL1 CEL1 CTL3 HAL3 0.0000 3 0.00 ! butene, adm jr., 2/00 update 441 | ! 1,4-dipentene, adm jr., 2/00 442 | CEL2 CEL1 CTL2 CEL1 1.200 1 180.00 !1,4-dipentene 443 | CEL2 CEL1 CTL2 CEL1 0.400 2 180.00 !1,4-dipentene 444 | CEL2 CEL1 CTL2 CEL1 1.300 3 180.00 !1,4-dipentene 445 | CEL1 CTL2 CEL1 HEL1 0.000 2 0.00 !1,4-dipentene 446 | CEL1 CTL2 CEL1 HEL1 0.000 3 0.00 !1,4-dipentene 447 | ! 2,5-diheptene, jbk., 9/2010 448 | ! for CIS double bonds in polyunsaturated lipids (default) 449 | CEL1 CEL1 CTL2 CEL1 0.850 1 180.00 !2,5-diheptane 450 | CEL1 CEL1 CTL2 CEL1 0.300 2 180.00 !2,5-diheptane 451 | CEL1 CEL1 CTL2 CEL1 0.260 3 0.00 !2,5-diheptane 452 | CEL1 CEL1 CTL2 CEL1 0.096 4 0.00 !2,5-diheptane 453 | ! for TRANS double bonds in polyunsaturated lipids 454 | ! uncomment following 4 lines and comment previous 4 lines to use 455 | !CEL1 CEL1 CTL2 CEL1 1.200 1 180.00 !2,5-diheptane 456 | !CEL1 CEL1 CTL2 CEL1 0.200 2 180.00 !2,5-diheptane 457 | !CEL1 CEL1 CTL2 CEL1 1.200 3 180.00 !2,5-diheptane 458 | !CEL1 CEL1 CTL2 CEL1 0.100 4 180.00 !2,5-diheptane 459 | 460 | ! 461 | IMPROPER 462 | ! 463 | !V(improper) = Kpsi(psi - psi0)**2 464 | ! 465 | !Kpsi: kcal/mole/rad**2 466 | !psi0: degrees 467 | !note that the second column of numbers (0) is ignored 468 | ! 469 | !atom types Kpsi psi0 470 | ! 471 | OBL X X CL 100.00 0 0.00 ! acetic acid 472 | HEL2 HEL2 CEL2 CEL2 3.00 0 0.00 ! ethene, yin,adm jr., 12/95 473 | OCL X X CL 96.00 0 0.00 ! acetate 474 | OCL X X CCL 96.00 0 0.00 ! for POPS 475 | 476 | 477 | NONBONDED nbxmod 5 atom cdiel fshift vatom vdistance vfswitch - 478 | cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5 479 | ! 480 | !V(Lennard-Jones) = Eps,i,j[(Rmin,i,j/ri,j)**12 - 2(Rmin,i,j/ri,j)**6] 481 | ! 482 | !epsilon: kcal/mole, Eps,i,j = sqrt(eps,i * eps,j) 483 | !Rmin/2: A, Rmin,i,j = Rmin/2,i + Rmin/2,j 484 | ! 485 | !atom ignored epsilon Rmin/2 ignored eps,1-4 Rmin/2,1-4 486 | ! 487 | HOL 0.0 -0.046 0.2245 488 | HAL1 0.0 -0.022 1.3200 ! alkane, 3/92 489 | HAL2 0.0 -0.028 1.3400 ! alkane, yin and mackerell, 4/98 490 | HAL3 0.0 -0.024 1.3400 ! alkane, yin and mackerell, 4/98 491 | HBL 0.0 -0.022 1.3200 ! for POPS 492 | HCL 0.0 -0.046 0.2245 ! ethanolamine 493 | HL 0.0 -0.046 0.7 ! polar H on NC4+ 494 | HEL1 0.0 -0.031 1.25 ! alkene, yin,adm jr., 12/95 495 | HEL2 0.0 -0.026 1.26 ! alkene, yin,adm jr., 12/95 496 | ! 497 | CL 0.0 -0.0700 2.00 ! methyl acetate update 498 | CCL 0.0 -0.0700 2.00 ! for POPS 499 | CTL1 0.0 -0.0200 2.275 0.0 -0.01 1.9 ! alkane, 3/92 500 | CTL2 0.0 -0.0560 2.010 0.0 -0.01 1.9 ! alkane, 4/98, yin, adm jr. 501 | CTL3 0.0 -0.0780 2.040 0.0 -0.01 1.9 ! alkane, 4/98, yin, adm jr. 502 | CTL5 0.0 -0.0800 2.06 0.0 -0.01 1.9 ! old CTL3 503 | ! maintained for tetramethylammonium 504 | CEL1 0.0 -0.068 2.09 ! alkene, yin,adm jr., 12/95 505 | CEL2 0.0 -0.064 2.08 ! alkene, yin,adm jr., 12/95 506 | CRL1 0.0 -0.0360 2.010 0.0 -0.01 1.9 ! CGAFF, jbk add for cholesterol 507 | CRL2 0.0 -0.0600 2.020 0.0 -0.01 1.9 ! CPEN, cyclopentane, 8/06 viv (jbk add) 508 | 509 | ! 510 | OBL 0.0 -0.12 1.70 0.0 -0.12 1.4 511 | OCL 0.0 -0.12 1.70 512 | O2L 0.0 -0.12 1.70 513 | OHL 0.0 -0.1521 1.77 514 | OSL 0.0 -0.1000 1.6500 !viv dec06 ether parameter 515 | OSLP 0.0 -0.1000 1.6500 !viv dec06 ether parameter 516 | ! 517 | NH3L 0.0 -0.20 1.85 ! ethanolamine 518 | NTL 0.0 -0.20 1.85 ! as all other nitogens 519 | ! 520 | SL 0.0 -0.47 2.1 ! methylsulfate 521 | PL 0.0 -0.585 2.15 ! ADM Jr. 522 | 523 | NBFIX 524 | ! Emin Rmin 525 | ! (kcal/mol) (A) 526 | ! 527 | 528 | HBOND CUTHB 0.5 ! If you want to do hbond analysis (only), then use 529 | ! READ PARAM APPEND CARD 530 | ! to append hbond parameters from the file: par_hbond.inp 531 | 532 | END 533 | -------------------------------------------------------------------------------- /tma-aco/Common/charmm/top_all36_na.rtf: -------------------------------------------------------------------------------- 1 | * \\\\ CHARMM36 All-Hydrogen Nucleic Acid Topology File //// 2 | * Alexander D. MacKerell Jr. and coworkers 3 | * April 2011 4 | * All comments to the CHARMM web site: www.charmm.org 5 | * parameter set discussion forum 6 | * 7 | 36 1 8 | 9 | !updated 2016/8. see toppar_all.history. 10 | 11 | !2010/2011 additions 12 | ! ejd, 2010 RNA update 13 | ! adm, 2011 DNA update 14 | ! For DNA update, new atom type required for P of DNA. This required 15 | ! replication of a number of parameters and the creation of new 16 | ! patches, DEOX and DEO5, to convert RNA to DNA, such that previous 17 | ! CHARMM scripts to generate DNA will no longer work. Note that the 18 | ! atom type change to P3 ONLY applies to the phosphodester linkage in 19 | ! DNA and NOT to terminal phosphates, DMP etc. 20 | ! 21 | 22 | !example of new generate/patch combination to generate DNA 23 | ! 24 | !read sequence card 25 | !* 1bna, strand 1 26 | !* 27 | !3 28 | !cyt gua cyt 29 | ! 30 | !generate a first 5ter last 3ter setup warn 31 | ! 32 | !patch deo5 a 1 setup warn !special patch for 5-terminal deoxy residue 33 | !patch deox a 2 setup warn !new patch to convert RNA to DNA 34 | !patch deox a 3 setup warn !no special patch required for 3-terminal deoxy residue 35 | ! 36 | !autogenerate angles dihedrals !Use of AUTOGENERATE is essential 37 | 38 | ! 39 | !references 40 | ! 41 | !NUCLEIC ACIDS 42 | ! 43 | !Denning, E.J., Priyakumar, U.D., Nilsson, L., and MacKerell Jr., A.D., 44 | !“Impact of 2’-hydroxyl sampling on the conformational properties of 45 | !RNA: Update of the CHARMM all-atom additive force field for RNA,” 46 | !JCC, 32: 1929-1943, 2011, PMC3082605 47 | ! 48 | !Hart, K., Foloppe, N., Baker, C.M., Denning, E.J., Nilsson, L. 49 | !and MacKerell Jr., A.D. “Optimization of the CHARMM additive force 50 | !field for DNA: Improved treatment of the BI/BII conformational 51 | !equilibrium,” JCTC, 8:348–362, 2012, PMC3285246 52 | ! 53 | 54 | !Foloppe, N. and MacKerell, Jr., A.D. "All-Atom Empirical Force Field for 55 | !Nucleic Acids: 1) Parameter Optimization Based on Small Molecule and 56 | !Condensed Phase Macromolecular Target Data. JCC, 2000, 21: 86-104. 57 | ! 58 | !MacKerell, Jr., A.D. and Banavali, N. "All-Atom Empirical Force Field for 59 | !Nucleic Acids: 2) Application to Molecular Dynamics Simulations of DNA 60 | !and RNA in Solution. JCC, 2000, 21: 105-120. 61 | ! 62 | 63 | 64 | MASS -1 HN1 1.00800 H ! Nucleic acid amine proton 65 | MASS -1 HN2 1.00800 H ! Nucleic acid ring nitrogen proton 66 | MASS -1 HN3 1.00800 H ! Nucleic acid aromatic carbon proton 67 | MASS -1 HN4 1.00800 H ! Nucleic acid phosphate hydroxyl proton 68 | MASS -1 HN5 1.00800 H ! Nucleic acid ribose hydroxyl proton 69 | MASS -1 HN6 1.00800 H ! Nucleic acid ribose aliphatic proton 70 | MASS -1 HN7 1.00800 H ! Nucleic acid proton (equivalent to protein HA) 71 | MASS -1 HN8 1.00800 H ! Bound to CN8 in nucleic acids/model compounds 72 | MASS -1 HN9 1.00800 H ! Bound to CN9 in nucleic acids/model compounds 73 | MASS -1 CN1 12.01100 C ! Nucleic acid carbonyl carbon 74 | MASS -1 CN1T 12.01100 C ! Nucleic acid carbonyl carbon (T/U C2) 75 | MASS -1 CN2 12.01100 C ! Nucleic acid aromatic carbon to amide 76 | MASS -1 CN3 12.01100 C ! Nucleic acid aromatic carbon 77 | MASS -1 CN3T 12.01100 C ! Nucleic acid aromatic carbon, Thy C5 78 | MASS -1 CN4 12.01100 C ! Nucleic acid purine C8 and ADE C2 79 | MASS -1 CN5 12.01100 C ! Nucleic acid purine C4 and C5 80 | MASS -1 CN5G 12.01100 C ! Nucleic acid guanine C5 81 | MASS -1 CN7 12.01100 C ! Nucleic acid carbon (equivalent to protein CT1) 82 | MASS -1 CN7B 12.01100 C ! Nucleic acid aliphatic carbon for C1' 83 | MASS -1 CN8 12.01100 C ! Nucleic acid carbon (equivalent to protein CT2) 84 | MASS -1 CN8B 12.01100 C ! Nucleic acid carbon (equivalent to protein CT2) 85 | MASS -1 CN9 12.01100 C ! Nucleic acid carbon (equivalent to protein CT3) 86 | MASS -1 NN1 14.00700 N ! Nucleic acid amide nitrogen 87 | MASS -1 NN2 14.00700 N ! Nucleic acid protonated ring nitrogen 88 | MASS -1 NN2B 14.00700 N ! From NN2, for N9 in GUA different from ADE 89 | MASS -1 NN2U 14.00700 N ! Nucleic acid protonated ring nitrogen, ura N3 90 | MASS -1 NN2G 14.00700 N ! Nucleic acid protonated ring nitrogen, gua N1 91 | MASS -1 NN3 14.00700 N ! Nucleic acid unprotonated ring nitrogen 92 | MASS -1 NN3A 14.00700 N ! Nucleic acid unprotonated ring nitrogen, ade N1 and N3 93 | MASS -1 NN3G 14.00700 N ! Nucleic acid unprotonated ring nitrogen, gua N3 94 | MASS -1 NN4 14.00700 N ! Nucleic acid purine N7 95 | MASS -1 NN6 14.00700 N ! Nucleic acid sp3 amine nitrogen (equiv to protein nh3) 96 | MASS -1 ON1 15.99940 O ! Nucleic acid carbonyl oxygen 97 | MASS -1 ON1C 15.99940 O ! Nucleic acid carbonyl oxygen, cyt O2 98 | MASS -1 ON2 15.99940 O ! Nucleic acid phosphate ester oxygen 99 | MASS -1 ON3 15.99940 O ! Nucleic acid =O in phosphate 100 | MASS -1 ON4 15.99940 O ! Nucleic acid phosphate hydroxyl oxygen 101 | MASS -1 ON5 15.99940 O ! Nucleic acid ribose hydroxyl oxygen 102 | MASS -1 ON6 15.99940 O ! Nucleic acid deoxyribose ring oxygen 103 | MASS -1 ON6B 15.99940 O ! Nucleic acid ribose ring oxygen 104 | MASS -1 P 30.97400 P ! phosphorus 105 | MASS -1 P2 30.97400 P ! phosphorus, adm, 2011 DNA update 106 | 107 | DECL +P 108 | DECL +O1P 109 | DECL +O2P 110 | DECL +O5' 111 | DECL -O3' 112 | 113 | DEFA FIRS none LAST none 114 | AUTOGENERATE ANGLES DIHEDRALS PATCH 115 | 116 | RESI GUA -1.00 ! O6 117 | ATOM P P 1.50 ! || 118 | ATOM O1P ON3 -0.78 ! C6 119 | ATOM O2P ON3 -0.78 ! / \ 120 | ATOM O5' ON2 -0.57 ! H1-N1 C5--N7\\ 121 | ATOM C5' CN8B -0.08 ! | || C8-H8 122 | ATOM H5' HN8 0.09 ! C2 C4--N9/ 123 | ATOM H5'' HN8 0.09 ! / \\ / \ 124 | GROUP ! H21-N2 N3 \ 125 | ATOM C4' CN7 0.16 ! | \ 126 | ATOM H4' HN7 0.09 ! H22 \ 127 | ATOM O4' ON6B -0.50 ! \ 128 | ATOM C1' CN7B 0.16 ! O1P H5' H4' O4' \ 129 | ATOM H1' HN7 0.09 ! | | \ / \ \ 130 | GROUP ! -P-O5'-C5'---C4' C1' 131 | ATOM N9 NN2B -0.02 ! | | \ / \ 132 | ATOM C4 CN5 0.26 ! O2P H5'' C3'--C2' H1' 133 | ATOM N2 NN1 -0.68 ! / \ / \ 134 | ATOM H21 HN1 0.32 ! O3' H3' O2' H2'' 135 | ATOM H22 HN1 0.35 ! | | 136 | ATOM N3 NN3G -0.74 ! H2' 137 | ATOM C2 CN2 0.75 138 | ATOM N1 NN2G -0.34 139 | ATOM H1 HN2 0.26 140 | ATOM C6 CN1 0.54 141 | ATOM O6 ON1 -0.51 142 | ATOM C5 CN5G 0.00 143 | ATOM N7 NN4 -0.60 144 | ATOM C8 CN4 0.25 145 | ATOM H8 HN3 0.16 146 | GROUP 147 | ATOM C2' CN7B 0.14 148 | ATOM H2'' HN7 0.09 149 | ATOM O2' ON5 -0.66 150 | ATOM H2' HN5 0.43 151 | GROUP 152 | ATOM C3' CN7 0.01 153 | ATOM H3' HN7 0.09 154 | ATOM O3' ON2 -0.57 155 | BOND P O1P P O2P P O5' 156 | BOND O5' C5' C5' C4' C4' O4' C4' C3' O4' C1' 157 | BOND C1' N9 C1' C2' N9 C4 N9 C8 C4 N3 158 | BOND C2 N2 C2 N1 N2 H21 159 | BOND N2 H22 N1 H1 N1 C6 C6 C5 160 | BOND C5 N7 C2' C3' C3' O3' O3' +P 161 | BOND C2' O2' O2' H2' 162 | BOND C1' H1' C2' H2'' C3' H3' C4' H4' C5' H5' 163 | BOND C5' H5'' C8 H8 164 | DOUBLE C2 N3 C4 C5 N7 C8 C6 O6 165 | IMPR C2 N3 N1 N2 C6 N1 C5 O6 N2 H21 C2 H22 166 | DONO H21 N2 167 | DONO H22 N2 168 | DONO H1 N1 169 | DONO H2' O2' 170 | ACCE O6 C6 171 | ACCE N3 172 | ACCE N7 173 | ACCE O1P P 174 | ACCE O2P P 175 | ACCE O2' 176 | ACCE O3' 177 | ACCE O4' 178 | ACCE O5' 179 | ! Chi and sugar-phosphate backbone in B-DNA like conformation 180 | BILD -O3' P O5' C5' 1.6001 101.45 -46.90 119.00 1.4401 !alpha 181 | BILD -O3' O5' *P O1P 1.6001 101.45 -115.82 109.74 1.4802 182 | BILD -O3' O5' *P O2P 1.6001 101.45 115.90 109.80 1.4801 183 | BILD P O5' C5' C4' 1.5996 119.00 -146.00 110.04 1.5160 !beta 184 | BILD O5' C5' C4' C3' 1.4401 108.83 60.00 116.10 1.5284 !gamma 185 | BILD C5' C4' C3' O3' 1.5160 116.10 140.00 115.12 1.4212 !delta 186 | BILD C4' C3' O3' +P 1.5284 111.92 155.00 119.05 1.6001 !epsilon 187 | BILD C3' O3' +P +O5' 1.4212 119.05 -95.20 101.45 1.5996 !zeta 188 | BILD O4' C3' *C4' C5' 1.4572 104.06 -120.04 116.10 1.5160 189 | BILD C2' C4' *C3' O3' 1.5284 100.16 -124.08 115.12 1.4212 190 | BILD C4' C3' C2' C1' 1.5284 100.16 -30.00 102.04 1.5251 !puck 191 | BILD C3' C2' C1' N9 1.5284 101.97 147.80 113.71 1.4896 192 | BILD O4' C1' N9 C4 1.5251 113.71 -97.2 125.59 1.3783 !chi 193 | BILD C1' C4 *N9 C8 1.4896 125.59 -179.99 106.0 1.374 194 | BILD C4 N9 C8 N7 1.377 106.0 0.0 113.5 1.304 195 | BILD C8 N9 C4 C5 1.374 106.0 0.0 105.6 1.377 196 | BILD N9 C5 *C4 N3 1.377 105.6 180.0 128.4 1.355 197 | BILD C5 C4 N3 C2 1.377 128.4 0.0 111.8 1.327 198 | BILD C4 N3 C2 N1 1.355 111.8 0.0 124.0 1.375 199 | BILD N1 N3 *C2 N2 1.375 124.0 180.0 119.7 1.341 200 | BILD N3 C2 N2 H21 1.327 119.7 180.0 127.0 1.01 201 | BILD H21 C2 *N2 H22 1.01 127.0 -180.0 116.5 1.01 202 | BILD N3 C2 N1 C6 1.327 124.0 0.0 124.9 1.393 203 | BILD C6 C2 *N1 H1 1.393 124.9 180.0 117.4 1.03 204 | BILD C5 N1 *C6 O6 1.415 111.7 180.0 120.0 1.239 205 | BILD N9 N7 *C8 H8 0.0 0.0 180.0 0.0 0.0 206 | BILD C1' C3' *C2' O2' 1.5284 102.04 -114.67 110.81 1.4212 207 | BILD H2' O2' C2' C3' 0.9600 114.97 148.63 111.92 1.5284 208 | BILD O4' C2' *C1' H1' 0.0 0.0 -115.0 0.0 0.0 209 | BILD C1' C3' *C2' H2'' 0.0 0.0 115.0 0.0 0.0 210 | BILD C2' C4' *C3' H3' 0.0 0.0 115.0 0.0 0.0 211 | BILD C3' O4' *C4' H4' 0.0 0.0 -115.0 0.0 0.0 212 | BILD C4' O5' *C5' H5' 0.0 0.0 -115.0 0.0 0.0 213 | BILD C4' O5' *C5' H5'' 0.0 0.0 115.0 0.0 0.0 214 | 215 | 216 | RESI ADE -1.00 ! H61 H62! 217 | ATOM P P 1.50 ! \ / 218 | ATOM O1P ON3 -0.78 ! N6 219 | ATOM O2P ON3 -0.78 ! | 220 | ATOM O5' ON2 -0.57 ! C6 221 | ATOM C5' CN8B -0.08 ! // \ 222 | ATOM H5' HN8 0.09 ! N1 C5--N7\\ 223 | ATOM H5'' HN8 0.09 ! | || C8-H8 224 | GROUP ! C2 C4--N9/ 225 | ATOM C4' CN7 0.16 ! / \\ / \ 226 | ATOM H4' HN7 0.09 ! H2 N3 \ 227 | ATOM O4' ON6B -0.50 ! \ 228 | ATOM C1' CN7B 0.16 ! \ 229 | ATOM H1' HN7 0.09 ! \ 230 | GROUP ! O1P H5' H4' O4' \ 231 | ATOM N9 NN2 -0.05 ! | | \ / \ \ 232 | ATOM C5 CN5 0.28 ! -P-O5'-C5'---C4' C1' 233 | ATOM N7 NN4 -0.71 ! | | \ / \ 234 | ATOM C8 CN4 0.34 ! O2P H5'' C3'--C2' H1' 235 | ATOM H8 HN3 0.12 ! / \ / \ 236 | ATOM N1 NN3A -0.74 ! O3' H3' O2' H2'' 237 | ATOM C2 CN4 0.50 ! | | 238 | ATOM H2 HN3 0.13 ! H2' 239 | ATOM N3 NN3A -0.75 240 | ATOM C4 CN5 0.43 241 | ATOM C6 CN2 0.46 242 | ATOM N6 NN1 -0.77 243 | ATOM H61 HN1 0.38 244 | ATOM H62 HN1 0.38 245 | GROUP 246 | ATOM C2' CN7B 0.14 247 | ATOM H2'' HN7 0.09 248 | ATOM O2' ON5 -0.66 249 | ATOM H2' HN5 0.43 250 | GROUP 251 | ATOM C3' CN7 0.01 252 | ATOM H3' HN7 0.09 253 | ATOM O3' ON2 -0.57 254 | BOND P O1P P O2P P O5' 255 | BOND O5' C5' C5' C4' C4' O4' C4' C3' O4' C1' 256 | BOND C1' N9 C1' C2' N9 C4 N9 C8 C4 N3 257 | BOND C2 N1 C6 N6 258 | BOND N6 H61 N6 H62 C6 C5 C5 N7 259 | BOND C2' C3' C2' O2' O2' H2' C3' O3' O3' +P 260 | BOND C1' H1' C2' H2'' C3' H3' C4' H4' C5' H5' 261 | BOND C5' H5'' C8 H8 C2 H2 262 | DOUBLE N1 C6 C2 N3 C4 C5 N7 C8 263 | IMPR N6 C6 H61 H62 C6 N1 C5 N6 264 | DONO H61 N6 265 | DONO H62 N6 266 | DONO H2' O2' 267 | ACCE N3 268 | ACCE N7 269 | ACCE N1 270 | ACCE O1P P 271 | ACCE O2P P 272 | ACCE O2' 273 | ACCE O3' 274 | ACCE O4' 275 | ACCE O5' 276 | BILD -O3' P O5' C5' 1.6001 101.45 -46.90 119.00 1.4401 !alpha 277 | BILD -O3' O5' *P O1P 1.6001 101.45 -115.82 109.74 1.4802 278 | BILD -O3' O5' *P O2P 1.6001 101.45 115.90 109.80 1.4801 279 | BILD P O5' C5' C4' 1.5996 119.00 -146.00 110.04 1.5160 !beta 280 | BILD O5' C5' C4' C3' 1.4401 108.83 60.00 116.10 1.5284 !gamma 281 | BILD C5' C4' C3' O3' 1.5160 116.10 140.00 115.12 1.4212 !delta 282 | BILD C4' C3' O3' +P 1.5284 111.92 155.00 119.05 1.6001 !epsilon 283 | BILD C3' O3' +P +O5' 1.4212 119.05 -95.20 101.45 1.5996 !zeta 284 | BILD O4' C3' *C4' C5' 1.4572 104.06 -120.04 116.10 1.5160 285 | BILD C2' C4' *C3' O3' 1.5284 100.16 -124.08 115.12 1.4212 286 | BILD C4' C3' C2' C1' 1.5284 100.16 -30.00 102.04 1.5251 !puck 287 | BILD C3' C2' C1' N9 1.5284 101.97 147.80 113.71 1.4896 288 | BILD O4' C1' N9 C4 1.5251 113.71 -97.2 125.59 1.3783 !chi 289 | BILD C1' C4 *N9 C8 1.4896 125.97 -179.94 106.0 1.367 290 | BILD C4 N9 C8 N7 1.376 106.0 0.0 113.6 1.312 291 | BILD C8 N9 C4 C5 1.367 106.0 0.0 105.6 1.382 292 | BILD C8 N7 C5 C6 0.0 0.0 180.0 0.0 0.0 293 | BILD N7 C5 C6 N1 0.0 0.0 180.0 0.0 0.0 294 | BILD C5 C6 N1 C2 0.0 0.0 0.0 0.0 0.0 295 | BILD N9 C5 *C4 N3 1.376 105.6 -180.0 126.9 1.342 296 | BILD C5 N1 *C6 N6 1.409 117.6 -180.0 121.2 1.337 297 | BILD N1 C6 N6 H61 1.337 121.2 0.0 119.0 1.01 298 | BILD H61 C6 *N6 H62 1.01 119.0 180.0 119.00 1.01 299 | BILD C5 N1 *C6 N6 1.409 117.6 -180.0 119.0 1.337 300 | BILD N1 C6 N6 H61 1.337 119.0 0.0 119.0 1.01 301 | BILD H61 C6 *N6 H62 1.01 119.0 180.0 121.00 1.01 302 | BILD N9 N7 *C8 H8 0.0 0.0 180.0 0.0 0.0 303 | BILD N1 N3 *C2 H2 0.0 0.0 180.0 0.0 0.0 304 | BILD C1' C3' *C2' O2' 1.5284 102.04 -114.67 110.81 1.4212 305 | BILD H2' O2' C2' C3' 0.9600 114.97 148.63 111.92 1.5284 306 | BILD O4' C2' *C1' H1' 0.0 0.0 -115.0 0.0 0.0 307 | BILD C1' C3' *C2' H2'' 0.0 0.0 115.0 0.0 0.0 308 | BILD C2' C4' *C3' H3' 0.0 0.0 115.0 0.0 0.0 309 | BILD C3' O4' *C4' H4' 0.0 0.0 -115.0 0.0 0.0 310 | BILD C4' O5' *C5' H5' 0.0 0.0 -115.0 0.0 0.0 311 | BILD C4' O5' *C5' H5'' 0.0 0.0 115.0 0.0 0.0 312 | 313 | RESI CYT -1.00 314 | ATOM P P 1.50 ! 315 | ATOM O1P ON3 -0.78 ! H42 H41 316 | ATOM O2P ON3 -0.78 ! \ / 317 | ATOM O5' ON2 -0.57 ! N4 318 | ATOM C5' CN8B -0.08 ! | 319 | ATOM H5' HN8 0.09 ! C4 320 | ATOM H5'' HN8 0.09 ! / \\ 321 | GROUP ! H5-C5 N3 322 | ATOM C4' CN7 0.16 ! || | 323 | ATOM H4' HN7 0.09 ! H6-C6 C2 324 | ATOM O4' ON6B -0.50 ! \ / \\ 325 | ATOM C1' CN7B 0.16 ! N1 O2 326 | ATOM H1' HN7 0.09 ! \ 327 | GROUP ! \ 328 | ATOM N1 NN2 -0.13 ! \ 329 | ATOM C6 CN3 0.05 ! O1P H5' H4' O4' \ 330 | ATOM H6 HN3 0.17 ! | | \ / \ \ 331 | ATOM C5 CN3 -0.13 ! -P-O5'-C5'---C4' C1' 332 | ATOM H5 HN3 0.07 ! | | \ / \ 333 | ATOM C2 CN1 0.52 ! O2P H5'' C3'--C2' H1' 334 | ATOM O2 ON1C -0.49 ! / \ / \ 335 | ATOM N3 NN3 -0.66 ! O3' H3' O2' H2'' 336 | ATOM C4 CN2 0.65 ! | | 337 | ATOM N4 NN1 -0.75 ! H2' 338 | ATOM H41 HN1 0.37 339 | ATOM H42 HN1 0.33 340 | GROUP 341 | ATOM C2' CN7B 0.14 342 | ATOM H2'' HN7 0.09 343 | ATOM O2' ON5 -0.66 344 | ATOM H2' HN5 0.43 345 | GROUP 346 | ATOM C3' CN7 0.01 347 | ATOM H3' HN7 0.09 348 | ATOM O3' ON2 -0.57 349 | BOND P O1P P O2P P O5' 350 | BOND O5' C5' C5' C4' C4' O4' C4' C3' O4' C1' 351 | BOND C1' N1 C1' C2' N1 C2 N1 C6 352 | BOND C2 N3 C4 N4 N4 H41 N4 H42 353 | BOND C4 C5 C2' C3' C3' O3' O3' +P 354 | BOND C2' O2' O2' H2' 355 | BOND C1' H1' C2' H2'' C3' H3' C4' H4' C5' H5' 356 | BOND C5' H5'' C5 H5 C6 H6 357 | DOUBLE C2 O2 C5 C6 N3 C4 358 | IMPR C2 N1 N3 O2 C4 N3 C5 N4 359 | IMPR N4 C4 H41 H42 360 | DONO H42 N4 361 | DONO H2' O2' 362 | DONO H41 N4 363 | ACCE O2 C2 364 | ACCE N3 365 | ACCE O1P P 366 | ACCE O2P P 367 | ACCE O2' 368 | ACCE O3' 369 | ACCE O4' 370 | ACCE O5' 371 | 372 | BILD -O3' P O5' C5' 1.6001 101.45 -46.90 119.00 1.4401 !alpha 373 | BILD -O3' O5' *P O1P 1.6001 101.45 -115.82 109.74 1.4802 374 | BILD -O3' O5' *P O2P 1.6001 101.45 115.90 109.80 1.4801 375 | BILD P O5' C5' C4' 1.5996 119.00 -146.00 110.04 1.5160 !beta 376 | BILD O5' C5' C4' C3' 1.4401 108.83 60.00 116.10 1.5284 !gamma 377 | BILD C5' C4' C3' O3' 1.5160 116.10 140.00 115.12 1.4212 !delta 378 | BILD C4' C3' O3' +P 1.5284 111.92 155.00 119.05 1.6001 !epsilon 379 | BILD C3' O3' +P +O5' 1.4212 119.05 -95.20 101.45 1.5996 !zeta 380 | BILD O4' C3' *C4' C5' 1.4572 104.06 -120.04 116.10 1.5160 381 | BILD C2' C4' *C3' O3' 1.5284 100.16 -124.08 115.12 1.4212 382 | BILD C4' C3' C2' C1' 1.5284 100.16 -30.00 102.04 1.5251 383 | BILD C3' C2' C1' N1 1.5284 101.97 147.89 113.71 1.4896 384 | BILD O4' C1' N1 C2 1.5251 113.71 -97.2 125.59 1.3783 !chi 385 | BILD C1' C2 *N1 C6 1.4896 117.79 -180.00 120.6 1.364 386 | BILD C2 N1 C6 C5 1.399 120.6 0.0 121.0 1.337 387 | BILD C6 N1 C2 N3 1.364 120.6 0.0 118.9 1.356 388 | BILD N1 N3 *C2 O2 1.399 118.9 180.0 121.9 1.237 389 | BILD N1 C2 N3 C4 1.399 118.9 0.0 120.0 1.334 390 | BILD C5 N3 *C4 N4 1.426 121.8 180.00 118.9 1.337 391 | BILD N3 C4 N4 H41 1.337 117.9 0.00 118.9 1.01 392 | BILD H41 C4 *N4 H42 1.01 118.9 180.00 120.7 1.01 393 | BILD C6 C4 *C5 H5 0.0 0.0 180.0 0.0 0.0 394 | BILD N1 C5 *C6 H6 0.0 0.0 180.0 0.0 0.0 395 | BILD C1' C3' *C2' O2' 1.5284 102.04 -114.67 110.81 1.4212 396 | BILD H2' O2' C2' C3' 0.9600 114.97 148.63 111.92 1.5284 397 | BILD O4' C2' *C1' H1' 0.0 0.0 -115.0 0.0 0.0 398 | BILD C1' C3' *C2' H2'' 0.0 0.0 115.0 0.0 0.0 399 | BILD C2' C4' *C3' H3' 0.0 0.0 115.0 0.0 0.0 400 | BILD C3' O4' *C4' H4' 0.0 0.0 -115.0 0.0 0.0 401 | BILD C4' O5' *C5' H5' 0.0 0.0 -115.0 0.0 0.0 402 | BILD C4' O5' *C5' H5'' 0.0 0.0 115.0 0.0 0.0 403 | 404 | RESI THY -1.00 ! H51 O4 405 | ATOM P P 1.50 ! | || 406 | ATOM O1P ON3 -0.78 ! H52-C5M C4 H3 407 | ATOM O2P ON3 -0.78 ! | \ / \ / 408 | ATOM O5' ON2 -0.57 ! H53 C5 N3 409 | ATOM C5' CN8B -0.08 ! || | 410 | ATOM H5' HN8 0.09 ! H6-C6 C2 411 | ATOM H5'' HN8 0.09 ! \ / \\ 412 | GROUP ! N1 O2 413 | ATOM C4' CN7 0.16 ! \ 414 | ATOM H4' HN7 0.09 ! \ 415 | ATOM O4' ON6B -0.50 ! \ 416 | ATOM C1' CN7B 0.16 ! O1P H5' H4' O4' \ 417 | ATOM H1' HN7 0.09 ! | | \ / \ \ 418 | GROUP ! -P-O5'-C5'---C4' C1' 419 | ATOM N1 NN2B -0.34 ! | | \ / \ 420 | ATOM C6 CN3 0.17 ! O2P H5'' C3'--C2' H1' 421 | ATOM H6 HN3 0.17 ! / \ / \ 422 | ATOM C2 CN1T 0.51 ! O3' H3' O2' H2'' 423 | ATOM O2 ON1 -0.41 ! | | 424 | ATOM N3 NN2U -0.46 ! H2' 425 | ATOM H3 HN2 0.36 ! 426 | ATOM C4 CN1 0.50 ! 427 | ATOM O4 ON1 -0.45 ! 428 | ATOM C5 CN3T -0.15 429 | ATOM C5M CN9 -0.11 430 | ATOM H51 HN9 0.07 431 | ATOM H52 HN9 0.07 432 | ATOM H53 HN9 0.07 433 | GROUP 434 | ATOM C2' CN7B 0.14 435 | ATOM H2'' HN7 0.09 436 | ATOM O2' ON5 -0.66 437 | ATOM H2' HN5 0.43 438 | GROUP 439 | ATOM C3' CN7 0.01 440 | ATOM H3' HN7 0.09 441 | ATOM O3' ON2 -0.57 442 | BOND P O1P P O2P P O5' 443 | BOND O5' C5' C5' C4' C4' O4' C4' C3' O4' C1' 444 | BOND C1' N1 C1' C2' N1 C2 N1 C6 445 | BOND C2 N3 N3 H3 N3 C4 C4 C5 446 | BOND C5 C5M C2' C3' C3' O3' O3' +P 447 | BOND C2' O2' O2' H2' 448 | BOND C1' H1' C2' H2'' C3' H3' C4' H4' C5' H5' 449 | BOND C5' H5'' C6 H6 C5M H51 C5M H52 C5M H53 450 | DOUBLE C2 O2 C4 O4 C5 C6 451 | IMPR C2 N1 N3 O2 C4 N3 C5 O4 C5 C4 C6 C5M 452 | DONO H3 N3 453 | DONO H2' O2' 454 | ACCE O2 C2 455 | ACCE O4 C4 456 | ACCE O1P P 457 | ACCE O2P P 458 | ACCE O2' 459 | ACCE O3' 460 | ACCE O4' 461 | ACCE O5' 462 | 463 | BILD -O3' P O5' C5' 1.6001 101.45 -46.90 119.00 1.4401 !alpha 464 | BILD -O3' O5' *P O1P 1.6001 101.45 -115.82 109.74 1.4802 465 | BILD -O3' O5' *P O2P 1.6001 101.45 115.90 109.80 1.4801 466 | BILD P O5' C5' C4' 1.5996 119.00 -146.00 110.04 1.5160 !beta 467 | BILD O5' C5' C4' C3' 1.4401 108.83 60.00 116.10 1.5284 468 | BILD C5' C4' C3' O3' 1.5160 116.10 140.00 115.12 1.4212 469 | BILD C4' C3' O3' +P 1.5284 111.92 155.00 119.05 1.6001 470 | BILD C3' O3' +P +O5' 1.4212 119.05 -95.20 101.45 1.5996 471 | BILD O4' C3' *C4' C5' 1.4572 104.06 -120.04 116.10 1.5160 472 | BILD C2' C4' *C3' O3' 1.5284 100.16 -124.08 115.12 1.4212 473 | BILD C4' C3' C2' C1' 1.5284 100.16 -30.00 102.04 1.5251 474 | BILD C3' C2' C1' N1 1.5284 101.97 147.89 113.71 1.4896 475 | BILD O4' C1' N1 C2 1.5251 113.71 -97.2 125.59 1.3783 !chi 476 | BILD C1' C2 *N1 C6 1.4896 117.06 -179.96 122.08 1.3704 477 | BILD C2 N1 C6 C5 1.3746 122.08 -0.02 121.23 1.3432 478 | BILD C6 N1 C2 N3 1.3704 122.08 0.06 115.38 1.3813 479 | BILD N1 N3 *C2 O2 1.3746 115.38 -179.95 121.70 1.2191 480 | BILD N1 C2 N3 C4 1.3746 115.38 -0.07 126.46 1.3795 481 | BILD C5 N3 *C4 O4 1.4439 114.07 179.98 120.59 1.2327 482 | BILD C2 C4 *N3 H3 1.3813 126.46 180.00 116.77 1.0900 483 | BILD C4 C6 *C5 C5M 1.4439 120.78 -179.94 121.63 1.5000 484 | BILD N1 C5 *C6 H6 0.0 0.0 180.0 0.0 0.0 485 | BILD C6 C5 C5M H51 0.0 0.0 0.0 0.0 0.0 486 | BILD C5 H51 *C5M H52 0.0 0.0 115.0 0.0 0.0 487 | BILD H51 H52 *C5M H53 0.0 0.0 -115.0 0.0 0.0 488 | BILD C1' C3' *C2' O2' 1.5284 102.04 -114.67 110.81 1.4212 489 | BILD H2' O2' C2' C3' 0.9600 114.97 148.63 111.92 1.5284 490 | BILD O4' C2' *C1' H1' 0.0 0.0 -115.0 0.0 0.0 491 | BILD C1' C3' *C2' H2'' 0.0 0.0 115.0 0.0 0.0 492 | BILD C2' C4' *C3' H3' 0.0 0.0 115.0 0.0 0.0 493 | BILD C3' O4' *C4' H4' 0.0 0.0 -115.0 0.0 0.0 494 | BILD C4' O5' *C5' H5' 0.0 0.0 -115.0 0.0 0.0 495 | BILD C4' O5' *C5' H5'' 0.0 0. 115.0 0.0 0.0 496 | 497 | RESI URA -1.00 ! O4 498 | ATOM P P 1.50 ! || 499 | ATOM O1P ON3 -0.78 ! C4 H3 500 | ATOM O2P ON3 -0.78 ! / \ / 501 | ATOM O5' ON2 -0.57 ! H5-C5 N3 502 | ATOM C5' CN8B -0.08 ! || | 503 | ATOM H5' HN8 0.09 ! H6-C6 C2 504 | ATOM H5'' HN8 0.09 ! \ / \\ 505 | GROUP ! N1 O2 506 | ATOM C4' CN7 0.16 ! \ 507 | ATOM H4' HN7 0.09 ! \ 508 | ATOM O4' ON6B -0.50 ! \ 509 | ATOM C1' CN7B 0.16 ! O1P H5' H4' O4' \ 510 | ATOM H1' HN7 0.09 ! | | \ / \ \ 511 | GROUP ! -P-O5'-C5'---C4' C1' 512 | ATOM N1 NN2B -0.34 ! | | \ / \ 513 | ATOM C6 CN3 0.20 ! O2P H5'' C3'--C2' H1' 514 | ATOM H6 HN3 0.14 ! / \ / \ 515 | ATOM C2 CN1T 0.55 ! O3' H3' O2' H2'' 516 | ATOM O2 ON1 -0.45 ! | | 517 | ATOM N3 NN2U -0.46 ! H2' 518 | ATOM H3 HN2 0.36 ! 519 | ATOM C4 CN1 0.53 ! 520 | ATOM O4 ON1 -0.48 ! 521 | ATOM C5 CN3 -0.15 ! 522 | ATOM H5 HN3 0.10 ! 523 | GROUP 524 | ATOM C2' CN7B 0.14 525 | ATOM H2'' HN7 0.09 526 | ATOM O2' ON5 -0.66 527 | ATOM H2' HN5 0.43 528 | GROUP 529 | ATOM C3' CN7 0.01 530 | ATOM H3' HN7 0.09 531 | ATOM O3' ON2 -0.57 532 | BOND P O1P P O2P P O5' 533 | BOND O5' C5' C5' C4' C4' O4' C4' C3' O4' C1' 534 | BOND C1' N1 C1' C2' N1 C2 N1 C6 535 | BOND C2 N3 N3 H3 N3 C4 C4 C5 536 | BOND C2' C3' C3' O3' O3' +P 537 | BOND C2' O2' O2' H2' 538 | BOND C1' H1' C2' H2'' C3' H3' C4' H4' C5' H5' 539 | BOND C5' H5'' C5 H5 C6 H6 540 | DOUBLE C2 O2 C4 O4 C5 C6 541 | IMPR C2 N1 N3 O2 C4 N3 C5 O4 542 | DONO H3 N3 543 | DONO H2' O2' 544 | ACCE O2 C2 545 | ACCE O4 C4 546 | ACCE O1P P 547 | ACCE O2P P 548 | ACCE O2' 549 | ACCE O3' 550 | ACCE O4' 551 | ACCE O5' 552 | BILD -O3' P O5' C5' 1.6001 101.45 -39.25 119.00 1.4401 553 | BILD -O3' O5' *P O1P 1.6001 101.45 -115.82 109.74 1.4802 554 | BILD -O3' O5' *P O2P 1.6001 101.45 115.90 109.80 1.4801 555 | BILD P O5' C5' C4' 1.5996 119.00 -151.39 110.04 1.5160 556 | BILD O5' C5' C4' C3' 1.4401 108.83 -179.85 116.10 1.5284 557 | BILD C5' C4' C3' O3' 1.5160 116.10 76.70 115.12 1.4212 558 | BILD C4' C3' O3' +P 1.5284 111.92 159.13 119.05 1.6001 559 | BILD C3' O3' +P +O5' 1.4212 119.05 -98.86 101.45 1.5996 560 | BILD O4' C3' *C4' C5' 1.4572 104.06 -120.04 116.10 1.5160 561 | BILD C2' C4' *C3' O3' 1.5284 100.16 -124.08 115.12 1.4212 562 | BILD C4' C3' C2' C1' 1.5284 100.16 39.58 102.04 1.5251 563 | BILD C3' C2' C1' N1 1.5284 101.97 144.39 113.71 1.4896 564 | BILD O4' C1' N1 C2 1.5251 113.71 -96.0 117.06 1.3746 565 | BILD C1' C2 *N1 C6 1.4896 117.06 -180.0 121.3 1.379 566 | BILD C2 N1 C6 C5 1.379 121.3 0.0 122.8 1.338 567 | BILD C6 N1 C2 N3 1.380 121.3 0.0 114.8 1.373 568 | BILD N1 N3 *C2 O2 1.379 114.8 -180.0 122.0 1.218 569 | BILD N1 C2 N3 C4 1.379 114.8 0.0 127.0 1.383 570 | BILD C5 N3 *C4 O4 1.440 114.7 180.0 119.8 1.227 571 | BILD C2 C4 *N3 H3 1.373 127.0 180.0 116.5 1.03 572 | BILD C6 C4 *C5 H5 0.0 0.0 180.0 0.0 0.0 573 | BILD N1 C5 *C6 H6 0.0 0.0 180.0 0.0 0.0 574 | BILD C1' C3' *C2' O2' 1.5284 102.04 -114.67 110.81 1.4212 575 | BILD H2' O2' C2' C3' 0.9600 114.97 148.63 111.92 1.5284 576 | BILD O4' C2' *C1' H1' 0.0 0.0 -115.0 0.0 0.0 577 | BILD C1' C3' *C2' H2'' 0.0 0.0 115.0 0.0 0.0 578 | BILD C2' C4' *C3' H3' 0.0 0.0 115.0 0.0 0.0 579 | BILD C3' O4' *C4' H4' 0.0 0.0 -115.0 0.0 0.0 580 | BILD C4' O5' *C5' H5' 0.0 0.0 -115.0 0.0 0.0 581 | BILD C4' O5' *C5' H5'' 0.0 0.0 115.0 0.0 0.0 582 | 583 | ! NOTE the option to regenerate all angles and dihedrals allows 584 | ! the explicit inclusion of the THET and DIHE terms to be omitted 585 | ! even if the PRES is used in a PATCH statement. It is important to 586 | ! inspect the patches prior to use to determine if they should be used 587 | ! in a GENErate or PATCh statement and/or if the AUTOgeneration of 588 | ! angles and dihedrals is required. 589 | ! see AUTOgen ANGLes DIHEdrals in STRUCTURE section of the 590 | ! documentation 591 | 592 | PRES DEO5 0.00 ! Patch to make the 5-terminal nucleotide into DEOXYribose 593 | DELETE ATOM O2' ! Follow with AUTOGENERATE ANGLES DIHEDRALS 594 | 595 | GROUP ! To correct O4' atom type in DNA (NF) 596 | ATOM C4' CN7 0.16 ! 597 | ATOM H4' HN7 0.09 ! 598 | ATOM O4' ON6 -0.50 ! 599 | ATOM C1' CN7B 0.16 ! 600 | ATOM H1' HN7 0.09 ! 601 | GROUP 602 | ATOM C2' CN8 -0.18 603 | ATOM H2' HN8 0.09 604 | ATOM H2'' HN8 0.09 605 | 606 | BOND C2' H2' 607 | BILD C1' C3' *C2' H2' 0.0 0.0 -115.0 0.0 0.0 608 | 609 | PRES DEOX 1.50 ! Patch to make non 5-terminal DEOXyribose nucleotides 610 | DELETE ATOM O2' ! Follow with AUTOGENERATE ANGLES DIHEDRALS 611 | 612 | ATOM P P2 1.50 ! switch type P to type P2 as required to apply 613 | ! 2011 DNA update to zeta in DNA only 614 | GROUP ! To correct O4' atom type in DNA (NF) 615 | ATOM C4' CN7 0.16 ! 616 | ATOM H4' HN7 0.09 ! 617 | ATOM O4' ON6 -0.50 ! 618 | ATOM C1' CN7B 0.16 ! 619 | ATOM H1' HN7 0.09 ! 620 | GROUP 621 | ATOM C2' CN8 -0.18 622 | ATOM H2' HN8 0.09 623 | ATOM H2'' HN8 0.09 624 | 625 | BOND C2' H2' 626 | BILD C1' C3' *C2' H2' 0.0 0.0 -115.0 0.0 0.0 627 | 628 | PRES DEOR 3.00 ! Patch to maintain a single RNA nucleotide in a DNA oligonucleotide 629 | ! Note that patch should be invoked once all the DEOX patches 630 | ! for the strand have been called 631 | ! 632 | ATOM P P2 1.50 ! switch type P to type P2 as required for DNA in i-1 nucleotide 633 | ATOM +P P 1.50 ! revert i+1 phosphorous from P2 to P type for RNA 634 | 635 | PRES 5TER 0.00 ! 5'-terminal HYDROXYL patch, from MeOH 636 | ! use in generate statement 637 | GROUP 638 | ATOM H5T HN5 0.43 639 | ATOM O5' ON5 -0.66 640 | ATOM C5' CN8B 0.05 641 | ATOM H5' HN8 0.09 642 | ATOM H5'' HN8 0.09 643 | ! 644 | DELETE ATOM P 645 | DELETE ATOM O1P 646 | DELETE ATOM O2P 647 | ! 648 | BOND H5T O5' 649 | DONO H5T O5' 650 | BILD H5T O5' C5' C4' 0.0000 0.00 180.00 0.00 0.0000 651 | 652 | PRES 5MET 0.00 ! 5'-ribose METHYL patch 653 | ! use in generate statement, doesn't work with DEOx patches 654 | GROUP 655 | ATOM C5' CN9 -0.27 656 | ATOM H5' HN9 0.09 657 | ATOM H5'' HN9 0.09 658 | ATOM H53' HN9 0.09 ! Can't use ''' and avoid conflict with THY 659 | ! 660 | DELETE ATOM O5' 661 | DELETE ATOM P 662 | DELETE ATOM O1P 663 | DELETE ATOM O2P 664 | ! 665 | BOND C5' H53' 666 | IC C3' C4' C5' H53' 0.0000 0.00 180.00 0.00 0.0000 667 | IC H53' C4' *C5' H5' 0.0000 0.00 120.00 0.00 0.0000 668 | IC H53' C4' *C5' H5'' 0.0000 0.00 -120.00 0.00 0.0000 669 | 670 | PRES 5PHO -1.00 ! 5'terminal PHOSPHATE patch 671 | ! use in generate statement 672 | GROUP 673 | ATOM C5' CN8B -0.08 674 | ATOM H5' HN8 0.09 675 | ATOM H5'' HN8 0.09 676 | ATOM P P 1.50 677 | ATOM O1P ON3 -0.82 678 | ATOM O2P ON3 -0.82 679 | ATOM O5' ON2 -0.62 680 | ATOM O5T ON4 -0.68 681 | ATOM H5T HN4 0.34 682 | BOND O5T P H5T O5T 683 | DONO H5T O5T 684 | ! Built in B-DNA-like conformation (NF) 685 | BILD C4' C5' O5' P 0.0000 000.00 -146.00 000.00 0.0000 686 | BILD C5' O5' P O5T 0.0000 000.00 -46.90 000.00 0.0000 687 | BILD O5T O5' *P O1P 0.0000 000.00 -115.82 000.00 0.0000 688 | BILD O5T O5' *P O2P 0.0000 000.00 115.90 000.00 0.0000 689 | BILD H5T O5T P O5' 0.0000 000.00 -95.20 000.00 0.0000 690 | 691 | PRES 5POM -1.00 ! 5'terminal Methyl-Phosphate patch 692 | ! use in generate statement 693 | GROUP 694 | ATOM C5' CN8B -0.08 695 | ATOM H5' HN8 0.09 696 | ATOM H5'' HN8 0.09 697 | ATOM P P 1.50 698 | ATOM O1P ON3 -0.78 699 | ATOM O2P ON3 -0.78 700 | ATOM O5' ON2 -0.57 701 | ATOM O5T ON2 -0.57 702 | ATOM C5T CN9 -0.17 703 | ATOM H5T1 HN9 0.09 704 | ATOM H5T2 HN9 0.09 705 | ATOM H5T3 HN9 0.09 706 | 707 | BOND O5T P O5T C5T C5T H5T1 C5T H5T2 708 | BOND C5T H5T3 709 | !DONO H5T O5T 710 | ! Built in B-DNA-like conformation (NF) 711 | BILD C4' C5' O5' P 0.0000 000.00 -146.00 000.00 0.0000 712 | BILD C5' O5' P O5T 0.0000 000.00 -46.90 000.00 0.0000 713 | BILD O5T O5' *P O1P 0.0000 000.00 -115.82 000.00 0.0000 714 | BILD O5T O5' *P O2P 0.0000 000.00 115.90 000.00 0.0000 715 | BILD C5T O5T P O5' 0.0000 000.00 -95.20 000.00 0.0000 716 | BILD H5T1 C5T O5T P 0.0000 000.00 180.20 000.00 0.0000 717 | BILD H5T2 C5T O5T P 0.0000 000.00 60.00 000.00 0.0000 718 | BILD H5T3 C5T O5T P 0.0000 000.00 -60.00 000.00 0.0000 719 | 720 | PRES 3TER 0.00 ! 3'terminal HYDROXYL patch, from MeOH 721 | ! use in generate statement 722 | GROUP 723 | ATOM C3' CN7 0.14 724 | ATOM H3' HN7 0.09 725 | ATOM O3' ON5 -0.66 726 | ATOM H3T HN5 0.43 727 | BOND O3' H3T 728 | DONO H3T O3' 729 | BILD H3T O3' C3' C4' 0.9600 114.97 148.63 111.92 1.5284 730 | 731 | PRES 3PHO -1.00 ! 3'terminal PHOSPHATE patch 732 | ! use in generate statement 733 | GROUP 734 | ATOM C3' CN7 0.01 735 | ATOM H3' HN7 0.09 736 | ATOM P3 P 1.50 737 | ATOM O1P3 ON3 -0.82 738 | ATOM O2P3 ON3 -0.82 739 | ATOM O3' ON2 -0.62 740 | ATOM O3T ON4 -0.68 741 | ATOM H3T HN4 0.34 742 | BOND O3' P3 P3 O1P3 P3 O2P3 P3 O3T O3T H3T 743 | DONO H3T O3T 744 | ACCE O3T 745 | ACCE O1P3 746 | ACCE O2P3 747 | ! Build in B-DNA-like conformation (NF) 748 | BILD C4' C3' O3' P3 0.0000 000.00 155.00 000.00 0.0000 749 | BILD C3' O3' P3 O3T 0.0000 000.00 -95.20 000.00 0.0000 750 | BILD O3T O3' *P3 O1P3 0.0000 000.00 -115.82 000.00 0.0000 751 | BILD O3T O3' *P3 O2P3 0.0000 000.00 115.90 000.00 0.0000 752 | BILD H3T O3T P3 O3' 0.0000 000.00 -46.90 000.00 0.0000 753 | 754 | PRES 3POM -1.00 ! 3'terminal Methyl Phosphate patch 755 | ! use in generate statement 756 | ! To build model compound with OPO3-CH3 at the 3' end (nicolas) 757 | GROUP 758 | ATOM C3' CN7 0.01 759 | ATOM H3' HN7 0.09 760 | ATOM P3 P 1.50 761 | ATOM O1P3 ON3 -0.78 762 | ATOM O2P3 ON3 -0.78 763 | ATOM O3' ON2 -0.57 764 | ATOM O3T ON2 -0.57 765 | ATOM C3T CN9 -0.17 766 | ATOM H3T1 HN9 0.09 767 | ATOM H3T2 HN9 0.09 768 | ATOM H3T3 HN9 0.09 769 | 770 | BOND O3' P3 P3 O1P3 P3 O2P3 P3 O3T O3T C3T 771 | BOND C3T H3T1 C3T H3T2 C3T H3T3 772 | ACCE O3' 773 | ACCE O5' 774 | ACCE O1P3 775 | ACCE O2P3 776 | BILD C4' C3' O3' P3 0.0000 000.00 155.00 000.00 0.0000 777 | BILD C3' O3' P3 O3T 0.0000 000.00 -95.22 000.00 0.0000 778 | BILD O3T O3' *P3 O1P3 0.0000 000.00 -115.82 000.00 0.0000 779 | BILD O3T O3' *P3 O2P3 0.0000 000.00 115.90 000.00 0.0000 780 | BILD C3T O3T P3 O3' 0.0000 000.00 -46.90 000.00 0.0000 781 | BILD H3T1 C3T O3T P3 0.0000 000.00 180.00 000.00 0.0000 782 | BILD H3T2 C3T O3T P3 0.0000 000.00 60.00 000.00 0.0000 783 | BILD H3T3 C3T O3T P3 0.0000 000.00 -60.00 000.00 0.0000 784 | 785 | PRES 3PO3 -2.00 ! 3'terminal PHOSPHATE patch 786 | ! use in generate statement 787 | ! Added by Nicolas, to be consistent with model componds 788 | GROUP 789 | ATOM C3' CN7 -0.09 790 | ATOM H3' HN7 0.09 791 | ATOM P3 P 1.10 792 | ATOM O3' ON2 -0.40 793 | ATOM O1P3 ON3 -0.90 794 | ATOM O2P3 ON3 -0.90 795 | ATOM O3P3 ON3 -0.90 796 | BOND O3' P3 P3 O1P3 P3 O2P3 P3 O3P3 797 | ACCE O1P3 798 | ACCE O2P3 799 | ACCE O3P3 800 | BILD C4' C3' O3' P3 0.0000 000.00 180.00 000.00 0.0000 801 | BILD C3' O3' P3 O3P3 0.0000 000.00 -39.52 000.00 0.0000 802 | BILD O3P3 O3' *P3 O1P3 0.0000 000.00 -115.82 000.00 0.0000 803 | BILD O3P3 O3' *P3 O2P3 0.0000 000.00 115.90 000.00 0.0000 804 | BILD O3' P3 O3P3 O3T 0.0000 000.00 180.00 000.00 0.0000 805 | BILD P3 O3P3 O3T H3T 0.0000 000.00 180.00 000.00 0.0000 806 | 807 | PRES DELB 0.00 ! patch to delete all possible base atoms 808 | ! of Cyt,Gua,Ade,Thy and Ura 809 | ! 810 | !note: error messages will be obtained due to atoms not present in 811 | !residue being "deleted" by this patch 812 | !cyt section 813 | DELE ATOM N1 814 | DELE ATOM C6 815 | DELE ATOM H6 816 | DELE ATOM C2 817 | DELE ATOM O2 818 | DELE ATOM N3 819 | DELE ATOM C4 820 | DELE ATOM N4 821 | DELE ATOM H41 822 | DELE ATOM H42 823 | DELE ATOM C5 824 | DELE ATOM H5 825 | !gua section 826 | DELE ATOM N9 827 | DELE ATOM H1 828 | DELE ATOM N2 829 | DELE ATOM H21 830 | DELE ATOM H22 831 | DELE ATOM O6 832 | DELE ATOM N7 833 | DELE ATOM C8 834 | DELE ATOM H8 835 | !ade section 836 | DELE ATOM H2 837 | DELE ATOM N6 838 | DELE ATOM H61 839 | DELE ATOM H62 840 | !thy/ura section 841 | DELE ATOM H3 842 | DELE ATOM O4 843 | DELE ATOM C5M 844 | DELE ATOM H51 845 | DELE ATOM H52 846 | DELE ATOM H53 847 | 848 | PRES CY35 0.0 ! patch to make a cyclic 3'-5' nucleotide 849 | ! use AUTOGEN ANGLE DIHE after this patch 850 | BOND O3' P ! but before water-generation 851 | 852 | PRES LKNA 0.0 ! Patch to join to nucleic acid segments (eg for IMAGES) 853 | ! eg: patch sega 10 segb 1 854 | ! sega should have std 3' (gene sega ... last none) 855 | ! segb should have std 5' (gene segb ... first none) 856 | ! USE AUTOgen ANGL DIHE after this patch, 857 | ! but before water-generation 858 | BOND 1O3' 2P 859 | IC 1O3' 2P 2O5' 2C5' 1.6001 101.45 -39.25 119.00 1.4401 860 | IC 1O3' 2O5' *2P 2O1P 1.6001 101.45 -115.82 109.74 1.4802 861 | IC 1O3' 2O5' *2P 2O2P 1.6001 101.45 115.90 109.80 1.4801 862 | IC 1C4' 1C3' 1O3' 2P 1.5284 111.92 159.13 119.05 1.6001 863 | IC 1C3' 1O3' 2P 2O5' 1.4212 119.05 -98.86 101.45 1.5996 864 | 865 | end 866 | 867 | -------------------------------------------------------------------------------- /tma-aco/Common/charmm/toppar_water_ions.str: -------------------------------------------------------------------------------- 1 | * Toplogy and parameter information for water and ions. 2 | * 3 | 4 | !Testcase 5 | !test_water_ions.inp 6 | 7 | ! IMPORTANT NOTE: this file contains NBFixes between carboxylates and sodium, 8 | ! which will only apply if the main files containing carboxylate atom types 9 | ! have been read in first! 10 | 11 | !references 12 | ! 13 | !TIP3P water model 14 | ! 15 | !W.L. Jorgensen; J.Chandrasekhar; J.D. Madura; R.W. Impey; 16 | !M.L. Klein; "Comparison of simple potential functions for 17 | !simulating liquid water", J. Chem. Phys. 79 926-935 (1983). 18 | ! 19 | !IONS 20 | ! 21 | !Ions from Roux and coworkers 22 | ! 23 | !Beglov, D. and Roux, B., Finite Representation of an Infinite 24 | !Bulk System: Solvent Boundary Potential for Computer Simulations, 25 | !Journal of Chemical Physics, 1994, 100: 9050-9063 26 | ! 27 | !ZINC 28 | ! 29 | !Stote, R.H. and Karplus, M. Zinc Binding in Proteins and 30 | !Solution: A Simple but Accurate Nonbonded Representation, PROTEINS: 31 | !Structure, Function, and Genetics 23:12-31 (1995) 32 | 33 | !test "append" to determine if previous toppar files have been read and 34 | !add append to "read rtf card" if true 35 | set nat ?NATC 36 | set app 37 | !We're exploiting what is arguably a bug in the parser. On the left hand side, 38 | !the quotes have priority, so NAT is correctly substituted. On the right hand 39 | !side, the ? has priority and NATC" (sic) is not a valid substitution... 40 | if "@NAT" ne "?NATC" if @nat ne 0 set app append 41 | 42 | read rtf card @app 43 | * Topology for water and ions 44 | * 45 | 31 1 46 | 47 | MASS -1 HT 1.00800 H ! TIPS3P WATER HYDROGEN 48 | MASS -1 HX 1.00800 H ! hydroxide hydrogen 49 | MASS -1 OT 15.99940 O ! TIPS3P WATER OXYGEN 50 | MASS -1 OX 15.99940 O ! hydroxide oxygen 51 | MASS -1 LIT 6.94100 LI ! Lithium ion 52 | MASS -1 SOD 22.98977 NA ! Sodium Ion 53 | MASS -1 MG 24.30500 MG ! Magnesium Ion 54 | MASS -1 POT 39.09830 K ! Potassium Ion 55 | MASS -1 CAL 40.08000 CA ! Calcium Ion 56 | MASS -1 RUB 85.46780 RB ! Rubidium Ion 57 | MASS -1 CES 132.90545 CS ! Cesium Ion 58 | MASS -1 BAR 137.32700 BA ! Barium Ion 59 | MASS -1 ZN 65.37000 ZN ! zinc (II) cation 60 | MASS -1 CAD 112.41100 CD ! cadmium (II) cation 61 | MASS -1 CLA 35.45000 CL ! Chloride Ion 62 | 63 | default first none last none 64 | 65 | RESI TIP3 0.000 ! tip3p water model, generate using noangle nodihedral 66 | GROUP 67 | ATOM OH2 OT -0.834 68 | ATOM H1 HT 0.417 69 | ATOM H2 HT 0.417 70 | BOND OH2 H1 OH2 H2 H1 H2 ! the last bond is needed for shake 71 | ANGLE H1 OH2 H2 ! required 72 | DONOR H1 OH2 73 | DONOR H2 OH2 74 | ACCEPTOR OH2 75 | PATCHING FIRS NONE LAST NONE 76 | 77 | RESI TP3M 0.000 ! "mmff" water model, as an analog of tip3p 78 | GROUP 79 | ATOM OH2 OT -0.834 ! these charges are replaced by the mmff setup 80 | ATOM H1 HT 0.417 ! these charges are replaced by the mmff setup 81 | ATOM H2 HT 0.417 ! these charges are replaced by the mmff setup 82 | BOND OH2 H1 OH2 H2 ! omits the H1-H2 bond, which is needed for shake with tip3p 83 | ANGLE H1 OH2 H2 ! required 84 | DONOR H1 OH2 85 | DONOR H2 OH2 86 | ACCEPTOR OH2 87 | PATCHING FIRS NONE LAST NONE 88 | 89 | RESI OH -1.00 ! hydroxide ion by adm.jr. 90 | GROUP 91 | ATOM O1 OX -1.32 92 | ATOM H1 HX 0.32 93 | BOND O1 H1 94 | DONOR H1 O1 95 | ACCEPTOR O1 96 | 97 | ! Ion parameters from Benoit Roux and Coworkers 98 | ! As of 8/10 new NBFIX terms required 99 | ! 100 | RESI LIT 1.00 ! Lithium Ion 101 | GROUP 102 | ATOM LIT LIT 1.00 103 | PATCHING FIRST NONE LAST NONE 104 | 105 | RESI SOD 1.00 ! Sodium Ion 106 | GROUP 107 | ATOM SOD SOD 1.00 108 | PATCHING FIRST NONE LAST NONE 109 | 110 | RESI MG 2.00 ! Magnesium Ion 111 | GROUP 112 | ATOM MG MG 2.00 113 | PATCHING FIRST NONE LAST NONE 114 | 115 | RESI POT 1.00 ! Potassium Ion 116 | GROUP 117 | ATOM POT POT 1.00 118 | PATCHING FIRST NONE LAST NONE 119 | 120 | RESI CAL 2.00 ! Calcium Ion 121 | GROUP 122 | ATOM CAL CAL 2.00 123 | PATCHING FIRST NONE LAST NONE 124 | 125 | RESI RUB 1.00 ! Rubidium Ion 126 | GROUP 127 | ATOM RUB RUB 1.00 128 | PATCHING FIRST NONE LAST NONE 129 | 130 | RESI CES 1.00 ! Cesium Ion 131 | GROUP 132 | ATOM CES CES 1.00 133 | PATCHING FIRST NONE LAST NONE 134 | 135 | RESI BAR 2.00 ! Barium Ion 136 | GROUP 137 | ATOM BAR BAR 2.00 138 | PATCHING FIRST NONE LAST NONE 139 | 140 | RESI ZN2 2.00 ! Zinc (II) cation, Roland Stote 141 | GROUP 142 | ATOM ZN ZN 2.00 143 | PATCHING FIRST NONE LAST NONE 144 | 145 | RESI CD2 2.00 ! Cadmium (II) cation 146 | GROUP 147 | ATOM CD CAD 2.00 148 | PATCHING FIRST NONE LAST NONE 149 | 150 | RESI CLA -1.00 ! Chloride Ion 151 | GROUP 152 | ATOM CLA CLA -1.00 153 | PATCHING FIRST NONE LAST NONE 154 | 155 | END 156 | 157 | read para card flex @app 158 | * Parameters for water and ions 159 | * 160 | 161 | ATOMS 162 | MASS -1 HT 1.00800 ! TIPS3P WATER HYDROGEN 163 | MASS -1 HX 1.00800 ! hydroxide hydrogen 164 | MASS -1 OT 15.99940 ! TIPS3P WATER OXYGEN 165 | MASS -1 OX 15.99940 ! hydroxide oxygen 166 | MASS -1 LIT 6.94100 ! Lithium ion 167 | MASS -1 SOD 22.98977 ! Sodium Ion 168 | MASS -1 MG 24.30500 ! Magnesium Ion 169 | MASS -1 POT 39.09830 ! Potassium Ion 170 | MASS -1 CAL 40.08000 ! Calcium Ion 171 | MASS -1 RUB 85.46780 ! Rubidium Ion 172 | MASS -1 CES 132.90545 ! Cesium Ion 173 | MASS -1 BAR 137.32700 ! Barium Ion 174 | MASS -1 ZN 65.37000 ! zinc (II) cation 175 | MASS -1 CAD 112.41100 ! cadmium (II) cation 176 | MASS -1 CLA 35.45000 ! Chloride Ion 177 | 178 | BONDS 179 | ! 180 | !V(bond) = Kb(b - b0)**2 181 | ! 182 | !Kb: kcal/mole/A**2 183 | !b0: A 184 | ! 185 | !atom type Kb b0 186 | ! 187 | HT HT 0.0 1.5139 ! from TIPS3P geometry (for SHAKE w/PARAM) 188 | HT OT 450.0 0.9572 ! from TIPS3P geometry 189 | OX HX 545.0 0.9700 ! hydroxide ion 190 | 191 | ANGLES 192 | ! 193 | !V(angle) = Ktheta(Theta - Theta0)**2 194 | ! 195 | !V(Urey-Bradley) = Kub(S - S0)**2 196 | ! 197 | !Ktheta: kcal/mole/rad**2 198 | !Theta0: degrees 199 | !Kub: kcal/mole/A**2 (Urey-Bradley) 200 | !S0: A 201 | ! 202 | !atom types Ktheta Theta0 Kub S0 203 | ! 204 | HT OT HT 55.0 104.52 ! FROM TIPS3P GEOMETRY 205 | 206 | DIHEDRALS 207 | ! 208 | !V(dihedral) = Kchi(1 + cos(n(chi) - delta)) 209 | ! 210 | !Kchi: kcal/mole 211 | !n: multiplicity 212 | !delta: degrees 213 | ! 214 | !atom types Kchi n delta 215 | ! 216 | 217 | 218 | ! 219 | IMPROPER 220 | ! 221 | !V(improper) = Kpsi(psi - psi0)**2 222 | ! 223 | !Kpsi: kcal/mole/rad**2 224 | !psi0: degrees 225 | !note that the second column of numbers (0) is ignored 226 | ! 227 | !atom types Kpsi psi0 228 | ! 229 | 230 | NONBONDED nbxmod 5 atom cdiel fshift vatom vdistance vfswitch - 231 | cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5 232 | 233 | !TIP3P LJ parameters 234 | HT 0.0 -0.046 0.2245 235 | OT 0.0 -0.1521 1.7682 236 | 237 | !for hydroxide 238 | OX 0.000000 -0.120000 1.700000 ! ALLOW POL ION 239 | ! JG 8/27/89 240 | HX 0.000000 -0.046000 0.224500 ! ALLOW PEP POL SUL ARO ALC 241 | ! same as TIP3P hydrogen, adm jr., 7/20/89 242 | 243 | !ions 244 | LIT 0.0 -0.00233 1.2975 ! Lithium 245 | ! From S Noskov, target ddG(Li-Na) was 23-26.0 kcal/mol (see JPC B, Lamoureux&Roux,2006) 246 | SOD 0.0 -0.0469 1.41075 ! new CHARMM Sodium 247 | ! ddG of -18.6 kcal/mol with K+ from S. Noskov 248 | MG 0.0 -0.0150 1.18500 ! Magnesium 249 | ! B. Roux dA = -441.65 250 | POT 0.0 -0.0870 1.76375 ! Potassium 251 | ! D. Beglovd and B. Roux, dA=-82.36+2.8 = -79.56 kca/mol 252 | CAL 0.0 -0.120 1.367 ! Calcium 253 | ! S. Marchand and B. Roux, dA = -384.8 kcal/mol 254 | RUB 0.0000 -0.15 1.90 ! Rubidium 255 | ! delta A with respect to POT is +6.0 kcal/mol in bulk water 256 | CES 0.0 -0.1900 2.100 ! Cesium 257 | ! delta A with respect to POT is +12.0 kcal/mol 258 | BAR 0.0 -0.150 1.890 ! Barium 259 | ! B. Roux, dA = dA[calcium] + 64.2 kcal/mol 260 | ZN 0.000000 -0.250000 1.090000 ! Zinc 261 | ! RHS March 18, 1990 262 | CAD 0.000000 -0.120000 1.357000 ! Cadmium 263 | ! S. Marchand and B. Roux, from delta delta G 264 | CLA 0.0 -0.150 2.27 ! Chloride 265 | ! D. Beglovd and B. Roux, dA=-83.87+4.46 = -79.40 kcal/mol 266 | 267 | NBFIX 268 | ! Emin Rmin 269 | ! (kcal/mol) (A) 270 | SOD CLA -0.083875 3.731 ! From osmotic pressure calibration, J. Phys.Chem.Lett. 1:183-189 271 | POT CLA -0.114236 4.081 ! From osmotic pressure calibration, J. Phys.Chem.Lett. 1:183-189 272 | END 273 | 274 | ! The following section contains NBFixes for sodium interacting with 275 | ! carboxylate oxygens of various CHARMM force fields. It will generate 276 | ! level -1 warnings whenever any of these force fields have not been 277 | ! read prior to the current stream file. Since we don't want to force 278 | ! the user to always read all the force fields, we're suppressing the 279 | ! warnings. The only side effect is that you will have "most severe 280 | ! warning was at level 0" at the end of your output. Also note that 281 | ! the user is responsible for reading the current file last if they 282 | ! want the NBFixes to apply. A more elegant solution would require new 283 | ! features to be added to CHARMM. 284 | ! parallel fix, to avoid duplicated messages in the log 285 | set para 286 | if ?NUMNODE gt 1 set para node 0 287 | 288 | set wrn ?WRNLEV 289 | ! Some versions of CHARMM don't seem to initialize wrnlev... 290 | if "@WRN" eq "?WRNLEV" set wrn 5 291 | set bom ?bomlev 292 | WRNLEV -1 @PARA 293 | BOMLEV -1 @PARA 294 | read para card flex append 295 | * NBFix between carboxylate and sodium 296 | * 297 | 298 | ! These NBFixes will only apply if the main files have been read in first!!! 299 | NBFIX 300 | 301 | !new SOD NBFIX values 302 | ! Simulations of Anionic Lipid Membranes: Development of Interaction-Specific 303 | ! Ion Parameters and Validation using NMR Data. 304 | ! Venable, R.M.; Luo, Y,; Gawrisch, K.; Roux, B.; Pastor, R.W. 305 | ! J. Phys. Chem. B 2013, 117 (35), pp 10183–10192. DOI: 10.1021/jp401512z 306 | ! 307 | ! prot 308 | SOD OC -0.07502 3.23 ! osmotic P; carboxylate =O 309 | SOD OS -0.07502 3.13 ! POPC optim.; ester =O 310 | !! NA 311 | !SOD ON3 -0.07502 3.16 ! POPC optim.; phosphate =O UNVALIDATED 312 | !! lipid 313 | SOD OCL -0.07502 3.23 ! osmotic P; carboxylate =O 314 | SOD OBL -0.07502 3.13 ! POPC optim.; ester =O 315 | SOD O2L -0.07502 3.16 ! POPC optim.; phosphate =O 316 | !! carb 317 | SOD OC2D2 -0.07502 3.23 ! osmotic P; carboxylate =O 318 | SOD OC2DP -0.07502 3.16 ! POPC optim.; phosphate =O 319 | !! CGenFF 320 | SOD OG2D2 -0.07502 3.23 ! osmotic P; carboxylate =O 321 | ! OG2D1 in CGenFF shared between esters, amides, aldehydes,... 322 | !SOD OG2D1 -0.07502 3.13 ! POPC optim.; ester =O 323 | SOD OG2P1 -0.07502 3.16 ! POPC optim.; phosphate =O 324 | 325 | END 326 | BOMLEV @bom @PARA 327 | WRNLEV @wrn @PARA 328 | 329 | return 330 | 331 | -------------------------------------------------------------------------------- /tma-aco/Common/common.namd: -------------------------------------------------------------------------------- 1 | # -*- tcl -*- 2 | 3 | set run [file rootname [file tail [info script]]] 4 | 5 | # set default options 6 | if { [info exists mol_name] == 0 } { 7 | set mol_name "tma-aco" 8 | set pbc "yes" 9 | if { [info exists coor_pdb_file] == 0 } { 10 | set coor_pdb_file "../Common/tma-aco.pdb" 11 | } 12 | set par_files [list \ 13 | "../Common/charmm/par_all36_cgenff.prm" \ 14 | "../Common/charmm/par_all36_prot.prm" \ 15 | "../Common/charmm/par_all36_lipid.prm" \ 16 | "../Common/charmm/par_all36_na.prm" \ 17 | "../Common/charmm/par_all36_carb.prm" \ 18 | "../Common/charmm/par_all36_cgenff.prm"] 19 | proc num_atoms {} { 20 | return 30 21 | } 22 | # source ../Common/delete_tmp_files.tcl 23 | # file link "index.ndx" "../Common/tma-cl.ndx" 24 | } 25 | 26 | if { [info exists output_name] == 0 } { 27 | set output_name "test" 28 | } 29 | 30 | if { [info exists temperature] == 0 } { 31 | set temperature 300.0 32 | } 33 | 34 | paraTypeCharmm on 35 | structure ../Common/${mol_name}.psf 36 | foreach par_file ${par_files} { 37 | parameters ${par_file} 38 | } 39 | 1-4scaling 1.0 40 | exclude scaled1-4 41 | rigidBonds all 42 | useSettle on 43 | 44 | switchdist 10.0 45 | cutoff 12.0 46 | pairlistdist 14.0 47 | fullElectFrequency 1 48 | nonbondedFreq 1 49 | 50 | coordinates "../Common/tma-aco.pdb" 51 | extendedSystem "../Common/tma-aco.xsc" 52 | if { [info exists coor_bin_file] > 0 } { 53 | binCoordinates ${coor_bin_file} 54 | } 55 | if { [info exists vel_bin_file] > 0 } { 56 | binVelocities ${vel_bin_file} 57 | } else { 58 | if { [info exists vel_pdb_file] > 0 } { 59 | velocities ${vel_pdb_file} 60 | } else { 61 | seed 87654321 62 | temperature ${temperature} 63 | } 64 | } 65 | 66 | COMmotion no 67 | zeroMomentum yes 68 | 69 | langevin on 70 | langevinTemp ${temperature} 71 | langevinDamping 10.0 72 | 73 | timestep 1.0 74 | 75 | outputName ${output_name} 76 | restartName ${output_name} 77 | restartFreq 100000 78 | if { [info exists pdb_restart] > 0 } { 79 | binaryRestart no 80 | binaryOutput no 81 | } else { 82 | binaryRestart yes 83 | binaryOutput yes 84 | } 85 | 86 | DCDfile ${output_name}.coor.dcd 87 | DCDfreq 1000 88 | DCDUnitCell yes 89 | 90 | outputEnergies 1000 91 | outputMomenta 1000 92 | outputPressure 1000 93 | outputTiming 1000 94 | 95 | 96 | if { [info exists numsteps] == 0 } { 97 | set numsteps 100000 98 | } 99 | -------------------------------------------------------------------------------- /tma-aco/Common/distance.colvars.in: -------------------------------------------------------------------------------- 1 | # Definition for distance variable 2 | 3 | colvar { 4 | name dist 5 | 6 | width 0.1 # Spacing of grids 7 | lowerBoundary 0.0 8 | upperBoundary 12.0 # Determined by size of unit cell used 9 | hardLowerBoundary yes # Inform biases that lower boundary won't be crossed 10 | hardUpperBoundary yes # Inform biases that upper boundary won't be crossed 11 | 12 | distance { 13 | group1 { atomNumbersRange 1-17 } 14 | group2 { atomNumbersRange 18-27 } 15 | } 16 | } 17 | -------------------------------------------------------------------------------- /tma-aco/Common/tma-aco.ndx: -------------------------------------------------------------------------------- 1 | [ Tetramethylammonium ] 2 | 1 2 3 4 5 6 7 8 3 | 9 10 11 12 13 14 15 16 4 | 17 5 | 6 | [ Acetone ] 7 | 18 19 20 21 22 23 24 25 8 | 26 27 9 | 10 | -------------------------------------------------------------------------------- /tma-aco/Common/tma-aco.pdb: -------------------------------------------------------------------------------- 1 | CRYST1 24.000 24.000 24.000 90.00 90.00 90.00 P 1 1 2 | ATOM 1 N NC4 N 1 -4.336 -0.384 0.140 0.00 0.00 NC4 3 | ATOM 2 C1 NC4 N 1 -3.697 -0.937 -1.096 0.00 0.00 NC4 4 | ATOM 3 C2 NC4 N 1 -5.823 -0.494 0.056 0.00 0.00 NC4 5 | ATOM 4 C3 NC4 N 1 -3.921 1.047 0.285 0.00 0.00 NC4 6 | ATOM 5 C4 NC4 N 1 -3.819 -1.147 1.320 0.00 0.00 NC4 7 | ATOM 6 H11 NC4 N 1 -2.624 -0.848 -1.019 0.00 0.00 NC4 8 | ATOM 7 H12 NC4 N 1 -4.013 -0.398 -1.977 0.00 0.00 NC4 9 | ATOM 8 H13 NC4 N 1 -3.937 -1.981 -1.230 0.00 0.00 NC4 10 | ATOM 9 H21 NC4 N 1 -6.131 -1.524 -0.048 0.00 0.00 NC4 11 | ATOM 10 H22 NC4 N 1 -6.205 0.054 -0.793 0.00 0.00 NC4 12 | ATOM 11 H23 NC4 N 1 -6.292 -0.096 0.945 0.00 0.00 NC4 13 | ATOM 12 H31 NC4 N 1 -4.240 1.637 -0.561 0.00 0.00 NC4 14 | ATOM 13 H32 NC4 N 1 -2.844 1.106 0.345 0.00 0.00 NC4 15 | ATOM 14 H33 NC4 N 1 -4.329 1.486 1.183 0.00 0.00 NC4 16 | ATOM 15 H41 NC4 N 1 -4.225 -0.765 2.245 0.00 0.00 NC4 17 | ATOM 16 H42 NC4 N 1 -2.744 -1.055 1.368 0.00 0.00 NC4 18 | ATOM 17 H43 NC4 N 1 -4.060 -2.197 1.248 0.00 0.00 NC4 19 | ATOM 18 O1 ACO A 1 -0.950 -0.102 0.351 0.00 0.00 ACO 20 | ATOM 19 C1 ACO A 1 0.272 0.021 0.402 0.00 0.00 ACO 21 | ATOM 20 C2 ACO A 1 1.190 -1.065 -0.046 0.00 0.00 ACO 22 | ATOM 21 C3 ACO A 1 0.915 1.266 0.913 0.00 0.00 ACO 23 | ATOM 22 H21 ACO A 1 1.845 -1.377 0.796 0.00 0.00 ACO 24 | ATOM 23 H22 ACO A 1 1.820 -0.702 -0.886 0.00 0.00 ACO 25 | ATOM 24 H23 ACO A 1 0.594 -1.938 -0.386 0.00 0.00 ACO 26 | ATOM 25 H31 ACO A 1 0.131 1.985 1.232 0.00 0.00 ACO 27 | ATOM 26 H32 ACO A 1 1.565 1.027 1.781 0.00 0.00 ACO 28 | ATOM 27 H33 ACO A 1 1.529 1.729 0.111 0.00 0.00 ACO 29 | END 30 | -------------------------------------------------------------------------------- /tma-aco/Common/tma-aco.psf: -------------------------------------------------------------------------------- 1 | PSF EXT 2 | 3 | 7 !NTITLE 4 | REMARKS original generated structure x-plor psf file 5 | REMARKS topology charmm/top_all36_prot.rtf 6 | REMARKS topology charmm/top_all36_lipid.rtf 7 | REMARKS topology charmm/top_all36_cgenff.rtf 8 | REMARKS topology charmm/top_water_ions.rtf 9 | REMARKS segment NC4 { first NONE; last NONE; auto angles dihedrals } 10 | REMARKS segment ACO { first NONE; last NONE; auto angles dihedrals } 11 | 12 | 27 !NATOM 13 | 1 NC4 1 NC4 N NG3P0 -0.600000 14.0070 0 14 | 2 NC4 1 NC4 C1 CG334 -0.350000 12.0110 0 15 | 3 NC4 1 NC4 C2 CG334 -0.350000 12.0110 0 16 | 4 NC4 1 NC4 C3 CG334 -0.350000 12.0110 0 17 | 5 NC4 1 NC4 C4 CG334 -0.350000 12.0110 0 18 | 6 NC4 1 NC4 H11 HGP5 0.250000 1.0080 0 19 | 7 NC4 1 NC4 H12 HGP5 0.250000 1.0080 0 20 | 8 NC4 1 NC4 H13 HGP5 0.250000 1.0080 0 21 | 9 NC4 1 NC4 H21 HGP5 0.250000 1.0080 0 22 | 10 NC4 1 NC4 H22 HGP5 0.250000 1.0080 0 23 | 11 NC4 1 NC4 H23 HGP5 0.250000 1.0080 0 24 | 12 NC4 1 NC4 H31 HGP5 0.250000 1.0080 0 25 | 13 NC4 1 NC4 H32 HGP5 0.250000 1.0080 0 26 | 14 NC4 1 NC4 H33 HGP5 0.250000 1.0080 0 27 | 15 NC4 1 NC4 H41 HGP5 0.250000 1.0080 0 28 | 16 NC4 1 NC4 H42 HGP5 0.250000 1.0080 0 29 | 17 NC4 1 NC4 H43 HGP5 0.250000 1.0080 0 30 | 18 ACO 1 ACO O1 OG2D3 -0.480000 15.9994 0 31 | 19 ACO 1 ACO C1 CG2O5 0.400000 12.0110 0 32 | 20 ACO 1 ACO C2 CG331 -0.230000 12.0110 0 33 | 21 ACO 1 ACO C3 CG331 -0.230000 12.0110 0 34 | 22 ACO 1 ACO H21 HGA3 0.090000 1.0080 0 35 | 23 ACO 1 ACO H22 HGA3 0.090000 1.0080 0 36 | 24 ACO 1 ACO H23 HGA3 0.090000 1.0080 0 37 | 25 ACO 1 ACO H31 HGA3 0.090000 1.0080 0 38 | 26 ACO 1 ACO H32 HGA3 0.090000 1.0080 0 39 | 27 ACO 1 ACO H33 HGA3 0.090000 1.0080 0 40 | 41 | 25 !NBOND: bonds 42 | 1 2 1 3 1 4 1 5 43 | 2 6 2 7 2 8 3 9 44 | 3 10 3 11 4 12 4 13 45 | 4 14 5 15 5 16 5 17 46 | 18 19 19 20 19 21 20 22 47 | 20 23 20 24 21 25 21 26 48 | 21 27 49 | 50 | 45 !NTHETA: angles 51 | 1 5 17 1 5 16 1 5 15 52 | 1 4 14 1 4 13 1 4 12 53 | 1 3 11 1 3 10 1 3 9 54 | 1 2 8 1 2 7 1 2 6 55 | 2 1 5 2 1 4 2 1 3 56 | 3 1 5 3 1 4 4 1 5 57 | 6 2 8 6 2 7 7 2 8 58 | 9 3 11 9 3 10 10 3 11 59 | 12 4 14 12 4 13 13 4 14 60 | 15 5 17 15 5 16 16 5 17 61 | 19 21 27 19 21 26 19 21 25 62 | 19 20 24 19 20 23 19 20 22 63 | 20 19 18 20 19 21 21 19 18 64 | 22 20 24 22 20 23 23 20 24 65 | 25 21 27 25 21 26 26 21 27 66 | 67 | 48 !NPHI: dihedrals 68 | 2 1 3 9 2 1 3 10 69 | 2 1 3 11 2 1 4 12 70 | 2 1 4 13 2 1 4 14 71 | 2 1 5 15 2 1 5 16 72 | 2 1 5 17 3 1 2 6 73 | 3 1 2 7 3 1 2 8 74 | 3 1 4 12 3 1 4 13 75 | 3 1 4 14 3 1 5 15 76 | 3 1 5 16 3 1 5 17 77 | 4 1 2 6 4 1 2 7 78 | 4 1 2 8 4 1 3 9 79 | 4 1 3 10 4 1 3 11 80 | 4 1 5 15 4 1 5 16 81 | 4 1 5 17 5 1 2 6 82 | 5 1 2 7 5 1 2 8 83 | 5 1 3 9 5 1 3 10 84 | 5 1 3 11 5 1 4 12 85 | 5 1 4 13 5 1 4 14 86 | 18 19 20 22 18 19 20 23 87 | 18 19 20 24 18 19 21 25 88 | 18 19 21 26 18 19 21 27 89 | 20 19 21 25 20 19 21 26 90 | 20 19 21 27 21 19 20 22 91 | 21 19 20 23 21 19 20 24 92 | 93 | 1 !NIMPHI: impropers 94 | 19 20 21 18 95 | 96 | 0 !NDON: donors 97 | 98 | 99 | 0 !NACC: acceptors 100 | 101 | 102 | 0 !NNB 103 | 104 | 0 0 0 0 0 0 0 0 105 | 0 0 0 0 0 0 0 0 106 | 0 0 0 0 0 0 0 0 107 | 0 0 0 108 | 109 | 1 0 !NGRP 110 | 0 0 0 111 | 112 | -------------------------------------------------------------------------------- /tma-aco/Common/tma-aco.xsc: -------------------------------------------------------------------------------- 1 | # NAMD extended system configuration output file 2 | #$LABELS step a_x a_y a_z b_x b_y b_z c_x c_y c_z o_x o_y o_z 3 | 0 24.000 0.000 0.000 0.000 24.000 0.000 0.000 0.000 24.000 0.000 0.000 0.000 4 | -------------------------------------------------------------------------------- /tma-aco/Common/write_index_file.tcl: -------------------------------------------------------------------------------- 1 | if { [string length [info procs write_index_group]] == 0 } { 2 | # Write a GROMACS-style .ndx file containing groups corresponding to atom 3 | # selections. Parameters: output (open file), sel (atomselect procedure), 4 | # label (name of the group) 5 | proc write_index_group { output sel label } { 6 | if { [${sel} num] == 0 } return 7 | puts "Writing index group \"${label}\": [${sel} num] atoms" 8 | puts ${output} [format "\[ %s \]" ${label}] 9 | set line_buf 0 10 | foreach num [${sel} get serial] { 11 | puts -nonewline ${output} [format " %9d" ${num}] 12 | set line_buf [expr ${line_buf} + 10] 13 | if { ${line_buf} > 70 } { 14 | set line_buf 0 15 | puts ${output} "" 16 | } 17 | } 18 | if { ${line_buf} > 0 } { 19 | puts ${output} "" 20 | } 21 | puts ${output} "" 22 | } 23 | } 24 | 25 | 26 | mol new tma-aco.psf type psf 27 | mol addfile tma-aco.pdb type pdb waitfor all 28 | 29 | if { [molinfo num] > 0 } { 30 | 31 | set ndx_file [open tma-aco.ndx "w"] 32 | 33 | write_index_group ${ndx_file} \ 34 | [atomselect top "segid NC4"] "Tetramethylammonium" 35 | write_index_group ${ndx_file} \ 36 | [atomselect top "segid ACO"] "Acetone" 37 | 38 | close ${ndx_file} 39 | } 40 | 41 | quit 42 | -------------------------------------------------------------------------------- /tma-aco/README.md: -------------------------------------------------------------------------------- 1 | This folder contains input files for a simulation of a tiny system (27 atoms) 2 | composed by one tetramethylammonium molecule and one acetone molecule. 3 | 4 | Files necessary to run the system with NAMD (force field, PSF/PDB, etc) are in 5 | the `Common` folder. 6 | 7 | Other folders contain inputs to run the most common biasing & sampling methods 8 | implemented by Colvars: 9 | 10 | - `smd`: Steered Molecular Dynamics, with integration of the work performed on 11 | the restraint center 12 | - `us`: umbrella sampling (WHAM inputs are not included) 13 | - `abf`: Adaptive Biasing Force (ABF), using the total-forces estimator 14 | (classic thermodynamic integration) 15 | - `mtd`: metadynamics 16 | 17 | ABF is directly based on thermodynamic integration (TI), but it is also 18 | possible to use the TI free energy estimator for other biases: add the keyword 19 | `writeTIPMF yes` to the configuration of the `harmonic` or `metadynamics` 20 | biases. 21 | -------------------------------------------------------------------------------- /tma-aco/abf/abf.namd: -------------------------------------------------------------------------------- 1 | # -*- tcl -*- 2 | 3 | # The output file name will be determined by the name of this script 4 | set output_name [file rootname [file tail [info script]]] 5 | 6 | set numsteps 100000 7 | 8 | source ../Common/common.namd 9 | 10 | colvars on 11 | 12 | cv configfile ../Common/distance.colvars.in 13 | 14 | set bias_conf " 15 | abf { 16 | name addy 17 | colvars dist 18 | fullSamples 10 19 | maxForce 50 20 | } 21 | " 22 | 23 | cv config ${bias_conf} 24 | 25 | run ${numsteps} 26 | 27 | -------------------------------------------------------------------------------- /tma-aco/mtd-ti/mtd-ti.namd: -------------------------------------------------------------------------------- 1 | # -*- tcl -*- 2 | 3 | # The output file name will be determined by the name of this script 4 | set output_name [file rootname [file tail [info script]]] 5 | 6 | set numsteps 100000 7 | 8 | source ../Common/common.namd 9 | 10 | colvars on 11 | 12 | cv configfile ../Common/distance.colvars.in 13 | 14 | set bias_conf " 15 | metadynamics { 16 | name metty 17 | colvars dist 18 | newHillFrequency 1 # This is a rather high frequency 19 | hillWeight 0.01 # This is a rather high strength 20 | hillWidth 1.0 # Note: this is a multiple of dist's width 21 | # The Gaussian half-width (sigma) will be printed on-screen) 22 | writeTIPMF yes 23 | } 24 | " 25 | 26 | cv config ${bias_conf} 27 | 28 | run ${numsteps} 29 | 30 | -------------------------------------------------------------------------------- /tma-aco/mtd/mtd.namd: -------------------------------------------------------------------------------- 1 | # -*- tcl -*- 2 | 3 | # The output file name will be determined by the name of this script 4 | set output_name [file rootname [file tail [info script]]] 5 | 6 | set numsteps 100000 7 | 8 | source ../Common/common.namd 9 | 10 | colvars on 11 | 12 | cv configfile ../Common/distance.colvars.in 13 | 14 | set bias_conf " 15 | metadynamics { 16 | name metty 17 | colvars dist 18 | newHillFrequency 1 # This is a rather high frequency 19 | hillWeight 0.01 # This is a rather high strength 20 | hillWidth 1.0 # Note: this is a multiple of dist's width 21 | # The Gaussian half-width (sigma) will be printed on-screen) 22 | } 23 | " 24 | 25 | cv config ${bias_conf} 26 | 27 | run ${numsteps} 28 | 29 | -------------------------------------------------------------------------------- /tma-aco/smd-ti/smd-ti.namd: -------------------------------------------------------------------------------- 1 | # -*- tcl -*- 2 | 3 | # The output file name will be determined by the name of this script 4 | set output_name [file rootname [file tail [info script]]] 5 | 6 | set numsteps 100000 7 | 8 | source ../Common/common.namd 9 | 10 | colvars on 11 | 12 | cv configfile ../Common/distance.colvars.in 13 | 14 | 15 | set bias_conf " 16 | harmonic { 17 | name steery 18 | colvars dist 19 | forceConstant 1.0 # Note: this will be rescaled by dist's width**2 20 | centers 4.0 21 | targetCenters 12.0 22 | targetNumSteps ${numsteps} 23 | outputCenters yes 24 | outputAccumulatedWork yes 25 | writeTIPMF yes 26 | } 27 | " 28 | 29 | cv config ${bias_conf} 30 | 31 | 32 | run ${numsteps} 33 | 34 | -------------------------------------------------------------------------------- /tma-aco/smd/smd.namd: -------------------------------------------------------------------------------- 1 | # -*- tcl -*- 2 | 3 | # The output file name will be determined by the name of this script 4 | set output_name [file rootname [file tail [info script]]] 5 | 6 | set numsteps 100000 7 | 8 | source ../Common/common.namd 9 | 10 | colvars on 11 | 12 | cv configfile ../Common/distance.colvars.in 13 | 14 | 15 | set bias_conf " 16 | harmonic { 17 | name steery 18 | colvars dist 19 | forceConstant 1.0 # Note: this will be rescaled by dist's width**2 20 | centers 4.0 21 | targetCenters 12.0 22 | targetNumSteps ${numsteps} 23 | outputCenters yes 24 | outputAccumulatedWork yes 25 | } 26 | " 27 | 28 | cv config ${bias_conf} 29 | 30 | 31 | run ${numsteps} 32 | 33 | -------------------------------------------------------------------------------- /tma-aco/test/test.namd: -------------------------------------------------------------------------------- 1 | # -*- tcl -*- 2 | 3 | # The output file name will be determined by the name of this script 4 | set output_name [file rootname [file tail [info script]]] 5 | 6 | set numsteps 100000 7 | 8 | source ../Common/common.namd 9 | 10 | # Add stuff here 11 | 12 | run ${numsteps} 13 | 14 | -------------------------------------------------------------------------------- /tma-aco/us-ti/us-ti.namd: -------------------------------------------------------------------------------- 1 | # -*- tcl -*- 2 | 3 | # The output file name will be determined by the name of this script 4 | set output_name [file rootname [file tail [info script]]] 5 | 6 | set numsteps 100000 7 | 8 | source ../Common/common.namd 9 | 10 | colvars on 11 | 12 | cv configfile ../Common/distance.colvars.in 13 | 14 | 15 | set bias_conf " 16 | harmonic { 17 | name umby 18 | colvars dist 19 | forceConstant 0.05 # Note: this will also be rescaled by dist's width**2 20 | centers 4.0 21 | targetCenters 12.0 22 | targetNumStages 9 23 | targetNumSteps [expr ${numsteps} / 9] 24 | outputCenters yes 25 | writeTIPMF yes 26 | } 27 | " 28 | 29 | cv config ${bias_conf} 30 | 31 | 32 | run ${numsteps} 33 | 34 | -------------------------------------------------------------------------------- /tma-aco/us/us.namd: -------------------------------------------------------------------------------- 1 | # -*- tcl -*- 2 | 3 | # The output file name will be determined by the name of this script 4 | set output_name [file rootname [file tail [info script]]] 5 | 6 | set numsteps 100000 7 | 8 | source ../Common/common.namd 9 | 10 | colvars on 11 | 12 | cv configfile ../Common/distance.colvars.in 13 | 14 | 15 | set bias_conf " 16 | harmonic { 17 | name umby 18 | colvars dist 19 | forceConstant 0.05 # Note: this will also be rescaled by dist's width**2 20 | centers 4.0 21 | targetCenters 12.0 22 | targetNumStages 9 23 | targetNumSteps [expr ${numsteps} / 9] 24 | outputCenters yes 25 | } 26 | " 27 | 28 | cv config ${bias_conf} 29 | 30 | 31 | run ${numsteps} 32 | 33 | --------------------------------------------------------------------------------