Error while running Lipid Tilt angle using a GRO file

[Muthukumaran R]

Dear users,

I have simulated POPE bilayer for 100 ns. I am performing Lipid Tilt analysis using membplugin in VMD between P and N atoms of head group, 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 message from vmd:

Something went wrong.

Command: lipidtilt -structure /home/kumaran/work/gromacs/mem_85/md_100ns.part0002.gro -trajectory /home/kumaran/work/gromacs/mem_85/md_100_frames.xtc -lipid {CHL1 SM18 DLPA DLPC DLPE DLPG DLPS DMPA DMPC DMPE DMPG
DMPS DPPA DPPC DPPE DPPG DPPS DSPA DSPC DSPE DSPG DSPS POPA POPC
POPE POPG POPS SOPA SOPC SOPE SOPS SOPG DOPA DOPC DOPE DOPG DOPS
SAPA SAPC SAPE SAPG SAPS SDPA SDPC SDPE SDPG SDPS DAPA DAPC DAPE
DAPG DAPS DXPC DXPE DXPS PLPC PLPE PLPS SLPC SLPE SLPS DGPC DGPE
DGPS DEPC DEPE DEPS DNPC DNPE DNPS PMPE PMPG QMPE OSPE PSPG IPPC
APPC PHPC} -diatom {{"POPE" "P N"}} -leaf {0 1} -from 0 -to last -step 1 -sel all -o /home/kumaran/work/gromacs/mem_85/md_100_frames.angles -wrapcmd {pbc wrap -center bb -centersel membplugin_lipid -compound res}

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/gromacs/mem_85/md_100ns.part0002.gro -trajectory /home/kumaran/work/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/gromacs/mem_85/md_100ns.part0002.gro -trajectory /home/kumaran/work/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/gromacs/mem_85/md_100ns.part0002.gro} -trajectory {/home/kumaran/work/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

[Ismael Rodriguez Espigares]

Dear Muthukumaran R,
The most likely explanation for the error that you found, taking into account that you are using a GRO file as topology file, is that VMD is not guessing correctly the connectivity of your POPE molecules and they get broken in some point.
These also might happen when using PDB files as topology. Also, your system must be wrapped in a way that molecules in PBC bounderies are not broken. Please, check requeriments regarding wrapping and loading topology in VMD at [GeneralRequirements] page.

Best,
Ismael.