Membrane thickness ERROR: Atom selection is empty.

[Alain Mutangana]

I am trying to compute thickness but I am encoutering this issue. I have my system wrapped and when I put my topology resname detail, it still ives me this

Something went wrong.

Command: membranethickness -structure E:/WaaL/Ecoli/centered_EcoliXTC_files/traj_files/EcoliWaal-1_PR_centered_nwt.gro -trajectory E:/WaaL/Ecoli/centered_EcoliXTC_files/traj_files/EcoliWaal-1_PR_centered_nwt.xtc -from 0 -to last -step 1 -sel {name P} -o E:/WaaL/Ecoli/centered_EcoliXTC_files/traj_files/EcoliWaal-1_PR_centered_nwt.thickness -wrapcmd {}

Error:
Atom selection is empty.
Atom selection is empty.
while executing
"error "Atom selection is empty.""
("uplevel" body line 8)
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 {

puts "Processing frame $f"

###Check atomselect
set ascheck [atomselect $..."
(procedure "::membranethickness::thickness" line 32)
invoked from within

"::membranethickness::thickness -structure E:/WaaL/Ecoli/centered_EcoliXTC_files/traj_files/EcoliWaal-1_PR_centered_nwt.gro -trajectory E:/WaaL/Ecoli/c..."
("eval" body line 1)
invoked from within
"eval ::membranethickness::thickness $args "
invoked from within
"if $errflag { error "Something went wrong.\n\nCommand: membranethickness $args\n\nError: \n$errMsg" $savedInfo $savedCode }"
(procedure "::membranethickness::membranethickness" line 26)
invoked from within
"::membranethickness::membranethickness -structure E:/WaaL/Ecoli/centered_EcoliXTC_files/traj_files/EcoliWaal-1_PR_centered_nwt.gro -trajectory E:/WaaL..."
("eval" body line 1)
invoked from within
"eval ::membranethickness::membranethickness $args"
(procedure "membranethickness" line 1)
invoked from within
"membranethickness -structure E:/WaaL/Ecoli/centered_EcoliXTC_files/traj_files/EcoliWaal-1_PR_centered_nwt.gro -trajectory E:/WaaL/Ecoli/centered_Ecoli..."
("eval" body line 1)
invoked from within
"eval $cmd"
(procedure "::membranethicknessgui::run" line 19)
invoked from within
"::membranethicknessgui::run"
invoked from within
".mtthicknessgui.nb.tavg.buttons.runbutton invoke "
invoked from within
".mtthicknessgui.nb.tavg.buttons.runbutton instate !disabled { .mtthicknessgui.nb.tavg.buttons.runbutton invoke } "
invoked from within
".mtthicknessgui.nb.tavg.buttons.runbutton instate pressed { .mtthicknessgui.nb.tavg.buttons.runbutton state !pressed; .mtthicknessgui.nb.tavg.buttons...."
(command bound to event)

[Ismael Rodriguez Espigares]

Dear Alain,
The only thing that can be failing is the atomselection that selects the phosphate atoms in your simulation. Your are running membrane thickness tool with the default "name P" atomselection.

Please, check that the phosphates in your simulation have as atom name "P", and that your structure (.gro) and trajectoriy (.xtc) files are loaded correctly by VMD, file paths E:/WaaL/Ecoli/centered_EcoliXTC_files/traj_files/EcoliWaal-1_PR_centered_nwt.gro and E:/WaaL/Ecoli/centered_EcoliXTC_files/traj_files/EcoliWaal-1_PR_centered_nwt.xtc by loading both files in the same VMD "molecule".

Update your atomselection so it selects all the phosphate atoms of your phopholipid membrane bilayer.