VMD-L Mailing List

From: Amir Zeb (zebamir85_at_gmail.com)
Date: Thu Aug 26 2021 - 02:03:51 CDT

Hello friends,

I want to compute the lipid tilt angles of a membrane simulation in vmd
from its dcd trajectory, but I got the following error while executing
the membplugin of vmd. Kindly let me know how to fix this error:

Error:
vecsub: two vectors don't have the same size
vecsub: two vectors don't have the same size
    while executing
"vecsub $B $A"
    (procedure "::membranetool_common::angle" line 7)
    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 {C:/Users/Amir/Desktop/BMDRC
data/Protocols/NAMD MD/MscL/Tanmay/server/charmgui/ionized.psf} -trajectory
{C:/Users/Amir/D..."
    ("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 {C:/Users/Amir/Desktop/BMDRC
data/Protocols/NAMD MD/MscL/Tanmay/server/charmgui/ionized.psf} -trajectory
{C:/Users/A..."
    ("eval" body line 1)
    invoked from within
"eval ::lipidtilt::lipidtilt $args"
    (procedure "lipidtilt" line 1)
    invoked from within
"lipidtilt -structure {C:/Users/Amir/Desktop/BMDRC data/Protocols/NAMD
MD/MscL/Tanmay/server/charmgui/ionized.psf} -trajectory
{C:/Users/Amir/Desktop/B..."
    ("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 24)
    invoked from within
"tk::ButtonUp .mttiltgui.run.button"
    (command bound to event)

I shall be thankful for your cooperation.

Regards!

Amir