I've already use the tool for the same membrane to analyze the production phase. Some results made me want to analyze the equilibration phase as well. I'm using the same triad of atoms as in the production analysis. The program runs until the frame 2105 (there are 5000 in total) and then shows this 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 /home/bulos/Desktop/respaldo/membrana/step5_charmm2amber.parm7 -trajectory /home/bulos/Desktop/respaldo/membrana/memtotal..."
("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 /home/bulos/Desktop/respaldo/membrana/step5_charmm2amber.parm7 -trajectory /home/bulos/Desktop/respaldo/membrana/mem..."
("eval" body line 1)
invoked from within
"eval ::lipidarea::lipidarea $args"
(procedure "lipidarea" line 1)
invoked from within
"lipidarea -structure {/home/bulos/Desktop/respaldo/membrana/step5_charmm2amber.parm7} -trajectory {/home/bulos/Desktop/respaldo/membrana/memtotal.dcd}..."
("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)
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
Dear Victor Daniel,
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 frame2105, please?
Otherwise, it will be difficult to replicate the error and check exactly what is failing.
In any case, you can just run the analysis from the frame 0 to 2014, and a second one from 2016 to 4999.
Thanks.
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
I've already use the tool for the same membrane to analyze the production phase. Some results made me want to analyze the equilibration phase as well. I'm using the same triad of atoms as in the production analysis. The program runs until the frame 2105 (there are 5000 in total) and then shows this error:
Something went wrong.
Command: lipidarea -structure /home/bulos/Desktop/respaldo/membrana/step5_charmm2amber.parm7 -trajectory /home/bulos/Desktop/respaldo/membrana/memtotal.dcd -triatom {{"POPE" "C2 C21 C31"} {"POPG" "C2 C21 C31"}} -leaf {0 1} -from 0 -to last -step 1 -qvoronoi /usr/local/lib/vmd/plugins/noarch/tcl/membplugin1.1/binaries/LINUXAMD64/qvoronoi -o /home/bulos/Desktop/respaldo/membrana/APL -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 /home/bulos/Desktop/respaldo/membrana/step5_charmm2amber.parm7 -trajectory /home/bulos/Desktop/respaldo/membrana/memtotal..."
("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 /home/bulos/Desktop/respaldo/membrana/step5_charmm2amber.parm7 -trajectory /home/bulos/Desktop/respaldo/membrana/mem..."
("eval" body line 1)
invoked from within
"eval ::lipidarea::lipidarea $args"
(procedure "lipidarea" line 1)
invoked from within
"lipidarea -structure {/home/bulos/Desktop/respaldo/membrana/step5_charmm2amber.parm7} -trajectory {/home/bulos/Desktop/respaldo/membrana/memtotal.dcd}..."
("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)
Dear Victor Daniel,
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 frame2105, please?
Otherwise, it will be difficult to replicate the error and check exactly what is failing.
In any case, you can just run the analysis from the frame 0 to 2014, and a second one from 2016 to 4999.
Thanks.