LipidTilt

The Lipid Tilt tool

This tool computes the angle between the vector defined by two lipid residue atoms and the Z axis.

1. Requirements

Lipid resnames definitions must be correctly set (see Main Window).
Also, see General Requirements.

2. Input

1. Resnames: residue names defining the lipid molecules to analyze. Default values are only examples for CHARMM-GUI. Important note: If several resnames are analyzed,
   "angle vs Frame" plot will show averages by frame of all specified lipid species, and the histogram will show the distribution of all the angles of all specified lipid species.
2. Atoms: atom names from lipid species in text box 1, that define the origin and destination of the tilt vector. Default values are only examples for CHARMM-GUI.
3. Atom selection: atom selection that set the residues to be analyzed. Default: “all” residues defined in "Resnames".
4. Leaflets: membrane leaflet to be analysed. “0” and “1” correspond to upper and bottom leaflets, respectively. If both are selected, an average between leaflets will be plotted in the "angle vs Frame" plot.
5. From: initial frame number.
6. To: last frame number.
7. Step: "step - 1" frames will be skipped at each iteration. One frame is analysed at each iteration.
8. Output file path: path to the output files, namely a "filename.angles" file suitable for external analysis, and a "filename.angles_plot~" temporary file with average angle values averaged per frame.

3. Output file format (tabulated)

filename.angles

Lipid       ResID   Residue Angle   Leaflet Frame
CHL1           1        268   4.912 0        4
CHL1           2        269   9.191 0        4
CHL1           3        270   9.588 0        4
CHL1           4        271   8.163 0        4
CHL1           5        272   8.218 0        4
CHL1           6        273  14.304 0        4
CHL1           7        274  20.251 0        4
CHL1           8        275  11.650 0        4
CHL1           9        276   1.337 0        4
CHL1          10        277   7.357 0        4
CHL1          11        278   3.332 0        4
CHL1          12        279  14.746 0        4
CHL1          13        280  19.956 0        4
CHL1          14        281   7.217 0        4
CHL1          15        282   3.594 0        4
CHL1          16        283   2.183 0        4
CHL1          17        284  16.754 0        4
CHL1          18        285  14.258 0        4
CHL1          19        286  10.634 0        4
CHL1          20        287  10.875 0        4
CHL1          21        288   2.204 0        4
CHL1          22        289  10.132 0        4
CHL1          23        290   4.803 0        4
CHL1          24        291   9.325 0        4
CHL1          25        292   2.073 0        4
CHL1          26        293  10.059 0        4
[...]

filename.angles_plot~

Frame   Angle   STD_Error
     4    9.510   0.483
     5    9.441   0.485
     6    9.508   0.491

• Lipid: residue name of each lipid species.
• ResID: resID of each residue.
• Residue: VMD internal residue number (useful when resID – resname pairs are not unique).
• Angle: tilt angle for each residue. In filename.angles_plot~, it is the average of each frame.
• STD_Error: standard error of each average tilt angle. In plot versus frames, SE is the average intragrupal standard error inside each frame, considering that number of lipids at each atom selection is the same inside each frame.
• Frame: frame number.
• Leaflet: “0” and “1” correspond to upper and bottom leaflets respectively.

[Muthukumaran R]

Dear Ismael,

I have simulated POPE bilayer for 100 ns. I am performing Lipid Tilt analysis using membplugin in VMD, but got the following error. I selected the input parameters as per tutorials. The lipid resname as 'POPE' and atoms for calculation as 'P N'

Error log.

Error:
vecdot needs vectors of the same size: 0 0 1 :
vecdot needs vectors of the same size: 0 0 1 :
while executing
"error "vecdot needs vectors of the same size: $x : $y""
(procedure "vecdot" line 3)
invoked from within
"vecdot $normal [vecnorm $CC]"
(procedure "::membranetool_common::angle" line 11)
invoked from within
"::membranetool_common::angle $atomcoord1 $atomcoord2 $normal"
(procedure "::lipidtilt::tilt_lip" line 51)
invoked from within
"::lipidtilt::tilt_lip [array get lipid_array] $nleaf $atomselection $FILE $FILE_plot $lipids $f"
("uplevel" body line 2)
invoked from within
"uplevel $block"
("while" body line 4)
invoked from within
"while $expression {
set pwvar $f
eval $wrapcmd
uplevel $block
animate delete all
incr f $step
mol addfile $dcd first $f last $f waitfor all
..."
(procedure "::membranetool_common::for_frames" line 19)
invoked from within
"::membranetool_common::for_frames $dcdfile $from $to $step f $wrapcmd {
::lipidtilt::tilt_lip [array get lipid_array] $nleaf $atomselection $FILE ..."
(procedure "::lipidtilt::tilt" line 91)
invoked from within
"::lipidtilt::tilt -structure /home/kumaran/work/NS1/gromacs/mem_85/md_100ns.part0002.gro -trajectory /home/kumaran/work/NS1/gromacs/mem_85/md_100_fram..."
("eval" body line 1)
invoked from within
"eval ::lipidtilt::tilt $args "
invoked from within
"if $errflag { error "Something went wrong.\n\nCommand: lipidtilt $args\n\nError: \n$errMsg" $savedInfo $savedCode }"
(procedure "::lipidtilt::lipidtilt" line 18)
invoked from within
"::lipidtilt::lipidtilt -structure /home/kumaran/work/NS1/gromacs/mem_85/md_100ns.part0002.gro -trajectory /home/kumaran/work/NS1/gromacs/mem_85/md_100..."
("eval" body line 1)
invoked from within
"eval ::lipidtilt::lipidtilt $args"
(procedure "lipidtilt" line 1)
invoked from within
"lipidtilt -structure {/home/kumaran/work/NS1/gromacs/mem_85/md_100ns.part0002.gro} -trajectory {/home/kumaran/work/NS1/gromacs/mem_85/md_100_frames.xt..."
("eval" body line 1)
invoked from within
"eval lipidtilt $command_line"
(procedure "::lipidtiltgui::tilt" line 85)
invoked from within
"::lipidtiltgui::tilt"
invoked from within
".mttiltgui.run.button invoke"
("uplevel" body line 1)
invoked from within
"uplevel #0 [list $w invoke]"
(procedure "tk::ButtonUp" line 22)
invoked from within
"tk::ButtonUp .mttiltgui.run.button"
(command bound to event)

Any help regarding how to use this module will be very helpful..

R. Muthukumaran