Recent changes to LipidTilt

Discussion for LipidTilt page

Muthukumaran R — Tue, 03 Jul 2018 13:03:53 -0000

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

LipidTilt modified by Ismael Rodriguez Espigares

Ismael Rodriguez Espigares — Wed, 26 Feb 2014 15:43:52 -0000

--- v28
+++ v29
@@ -21,11 +21,8 @@
 * __Step__:  "step - 1" frames will be skipped at each iteration. One frame is analysed at each iteration.
 * __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. Tutorial

-(Work in progress)
-
-##4. Output file format (tabulated)
+##3. Output file format (tabulated)

 _filename_.angles

LipidTilt modified by Toni

Toni — Thu, 19 Dec 2013 15:48:12 -0000

--- v27
+++ v28
@@ -5,7 +5,7 @@
 ##1. Requirements

 __Lipid resnames__ definitions must be correctly set (see [Main Window](GUIMainwindow)).
-Also, see [General Requeriments](GeneralRequirements).
+Also, see [General Requirements](GeneralRequirements).

 ##2. Input

LipidTilt modified by Ismael Rodriguez Espigares

Ismael Rodriguez Espigares — Fri, 29 Nov 2013 13:18:46 -0000

--- v26
+++ v27
@@ -77,6 +77,6 @@
 * __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. 
+* __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.

LipidTilt modified by Ismael Rodriguez Espigares

Ismael Rodriguez Espigares — Thu, 28 Nov 2013 17:40:22 -0000

--- v25
+++ v26
@@ -77,6 +77,6 @@
 * __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.
+* __STD\_Error__: standard error of each average tilt angle. In plot versus frames, SE is the average intragrupal standard error inside each frame. 
 * __Frame__: frame number.
 * __Leaflet__: “0” and “1” correspond to upper and bottom leaflets respectively.

LipidTilt modified by Ismael Rodriguez Espigares

Ismael Rodriguez Espigares — Thu, 10 Oct 2013 10:26:51 -0000

--- v24
+++ v25
@@ -57,6 +57,7 @@
 CHL1         24        291   9.325 0        4
 CHL1         25        292   2.073 0        4
 CHL1         26        293  10.059 0        4
+[...]
 ~~~~~

LipidTilt modified by Ramon Guixa

Ramon Guixa — Tue, 08 Oct 2013 16:55:32 -0000

--- v23
+++ v24
@@ -18,7 +18,7 @@
 * __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.
 * __From__: initial frame number.
 * __To__: last frame number.
-* __Step__:  "step - 1" frames will be skipped at every iteration. One frame is analysed at each iteration.
+* __Step__:  "step - 1" frames will be skipped at each iteration. One frame is analysed at each iteration.
 * __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. Tutorial

LipidTilt modified by Ramon Guixa

Ramon Guixa — Tue, 08 Oct 2013 16:47:45 -0000

--- v22
+++ v23
@@ -19,8 +19,7 @@
 * __From__: initial frame number.
 * __To__: last frame number.
 * __Step__:  "step - 1" frames will be skipped at every iteration. One frame is analysed at each iteration.
-* __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 by frame.
-
+* __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. Tutorial

LipidTilt modified by Ramon Guixa

Ramon Guixa — Tue, 08 Oct 2013 16:44:19 -0000

--- v21
+++ v22
@@ -14,12 +14,12 @@
 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.
 * __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__.
-* __Atom selection__: atom selection to choose which residues will be analyzed. __Default__: “all” residues defined in "Resnames".
-* __Leaflets__: selection of membrane leaflets that will be analyzed. “0” and “1” correspond to upper and bottom leaflets respectively. If both are selected, the average between leaflets will be plot in "angle vs Frame" plot.
+* __Atom selection__: atom selection that set the residues to be analyzed. __Default__: “all” residues defined in "Resnames".
+* __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.
 * __From__: initial frame number.
-* __To__: last frame number. To analyze until the last frame, type “last”.
-* __Step__:  "step - 1" frames will be skipped at every iteration. One frame is analysed at every iteration.
-* __Output file path__: path to the output files that will be created. 2 files will be generated, a _filename_.angles file suitable for external analysis, and a _filename_.angles_plot~ temporary file with angle means by frame.
+* __To__: last frame number.
+* __Step__:  "step - 1" frames will be skipped at every iteration. One frame is analysed at each iteration.
+* __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 by frame.

 ##3. Tutorial

LipidTilt modified by Ismael Rodriguez Espigares

Ismael Rodriguez Espigares — Tue, 08 Oct 2013 11:11:43 -0000

--- v20
+++ v21
@@ -18,7 +18,7 @@
 * __Leaflets__: selection of membrane leaflets that will be analyzed. “0” and “1” correspond to upper and bottom leaflets respectively. If both are selected, the average between leaflets will be plot in "angle vs Frame" plot.
 * __From__: initial frame number.
 * __To__: last frame number. To analyze until the last frame, type “last”.
-* __Step__:  "step - 1" frames will be skipped at each step.  One frame is analysed at every step.
+* __Step__:  "step - 1" frames will be skipped at every iteration. One frame is analysed at every iteration.
 * __Output file path__: path to the output files that will be created. 2 files will be generated, a _filename_.angles file suitable for external analysis, and a _filename_.angles_plot~ temporary file with angle means by frame.