I am trying to calculate the APL of my bilayer. It is heterogenous, but I have defined the atom triad following the default MEMBPLUGIN settings / as recommended by the wiki page.
The calculation runs and outputs fine from frames 1 to 919.
Then fails on frame 920 with the following error:
Error:
can't use non-numeric string as operand of ""
can't use non-numeric string as operand of ""
while executing
"* $x1 $y2"
(procedure "::lipidarea::polarea" line 37)
invoked from within
"::lipidarea::polarea $regions $vertices"
(procedure "::lipidarea::compute_area" line 63)
invoked from within
"::lipidarea::compute_area $outputfile $triatoms $nleaf $qvoronoipath $FILE1 $FILE2 [array get lipid_array] $lipids $f"
("uplevel" body line 3)
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 {
(procedure "::lipidarea::area" line 136)
invoked from within
"::lipidarea::area -structure step5_charmm2gmx.psf -trajectory step7all_every1ns_whole.xtc -triatom {{"SDPC SAPC POPC DPPC PLPC SDPE SAPE SLPE SOP..."
("eval" body line 1)
invoked from within
"eval ::lipidarea::area $args "
invoked from within
"if $errflag { error "Something went wrong.\n\nCommand: lipidarea $args\n\nError: \n$errMsg" $savedInfo $savedCode }"
(procedure "::lipidarea::lipidarea" line 17)
invoked from within
"::lipidarea::lipidarea -structure step5_charmm2gmx.psf -trajectory step7all_every1ns_whole.xtc -triatom {{"SDPC SAPC POPC DPPC PLPC SDPE SAPE SLP..."
("eval" body line 1)
invoked from within
"eval ::lipidarea::lipidarea $args"
(procedure "lipidarea" line 1)
invoked from within
"lipidarea -structure {step5_charmm2gmx.psf} -trajectory {step7all_every1ns_whole.xtc} -triatom {{"SDPC SAPC POPC DPPC PLPC SDPE SAPE SLPE SOPE DS..."
("eval" body line 1)
invoked from within
"eval lipidarea $command_line"
(procedure "::lipidareagui::area" line 74)
invoked from within
"::lipidareagui::area"
invoked from within
".mtareagui.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 .mtareagui.run.button"
(command bound to event)
Please kindly advise.
Many thanks.
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
Dear Physics,
Probably, that specific frame might be tricky for qvoronoi tessellation for some reason. Could you send us your PSF file and an XTC file with this frame 920, please?
Otherwise, it will be difficult to replicate the error and check exactly what is failing.
Thanks.
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
Dear all,
I am trying to calculate the APL of my bilayer. It is heterogenous, but I have defined the atom triad following the default MEMBPLUGIN settings / as recommended by the wiki page.
The calculation runs and outputs fine from frames 1 to 919.
Then fails on frame 920 with the following error:
Something went wrong.
Command: lipidarea -structure step5_charmm2gmx.psf -trajectory step7all_every1ns_whole.xtc -triatom {{"SDPC SAPC POPC DPPC PLPC SDPE SAPE SLPE SOPE DSPE SDPS SOPS SAPI25 PNPI25 POPI25" "C2 C21 C31"} {"ASM NSM CER180 CER200 CER240 CER241" "C2S C1F C3S"} {"CHL1" "O3"}} -leaf {0 1} -from 920 -to last -step 1 -qvoronoi /opt/vmd/lib/vmd/plugins/noarch/tcl/membplugin1.1/binaries/LINUXAMD64/qvoronoi -o /analysis_apl_MEMB/apl_MEMB_920to1000 -wrapcmd {}
Error:
can't use non-numeric string as operand of ""
can't use non-numeric string as operand of ""
while executing
"* $x1 $y2"
(procedure "::lipidarea::polarea" line 37)
invoked from within
"::lipidarea::polarea $regions $vertices"
(procedure "::lipidarea::compute_area" line 63)
invoked from within
"::lipidarea::compute_area $outputfile $triatoms $nleaf $qvoronoipath $FILE1 $FILE2 [array get lipid_array] $lipids $f"
("uplevel" body line 3)
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 {
"::lipidarea::area -structure step5_charmm2gmx.psf -trajectory step7all_every1ns_whole.xtc -triatom {{"SDPC SAPC POPC DPPC PLPC SDPE SAPE SLPE SOP..."
("eval" body line 1)
invoked from within
"eval ::lipidarea::area $args "
invoked from within
"if $errflag { error "Something went wrong.\n\nCommand: lipidarea $args\n\nError: \n$errMsg" $savedInfo $savedCode }"
(procedure "::lipidarea::lipidarea" line 17)
invoked from within
"::lipidarea::lipidarea -structure step5_charmm2gmx.psf -trajectory step7all_every1ns_whole.xtc -triatom {{"SDPC SAPC POPC DPPC PLPC SDPE SAPE SLP..."
("eval" body line 1)
invoked from within
"eval ::lipidarea::lipidarea $args"
(procedure "lipidarea" line 1)
invoked from within
"lipidarea -structure {step5_charmm2gmx.psf} -trajectory {step7all_every1ns_whole.xtc} -triatom {{"SDPC SAPC POPC DPPC PLPC SDPE SAPE SLPE SOPE DS..."
("eval" body line 1)
invoked from within
"eval lipidarea $command_line"
(procedure "::lipidareagui::area" line 74)
invoked from within
"::lipidareagui::area"
invoked from within
".mtareagui.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 .mtareagui.run.button"
(command bound to event)
Please kindly advise.
Many thanks.
Dear Physics,
Probably, that specific frame might be tricky for qvoronoi tessellation for some reason. Could you send us your PSF file and an XTC file with this frame 920, please?
Otherwise, it will be difficult to replicate the error and check exactly what is failing.
Thanks.