Error with Shape Based CG Model

From: Anirban Ghosh (
Date: Wed Aug 06 2008 - 05:04:27 CDT

Hi All,
I am trying to generate a Shape-based CG model of a protein with 456
residues through CG Builder plug-in of VMD. I tried with the default
parameters and 15 and 30 CG beads, twice. But I am getting the following
error every time:

atomsel: frame -1 out of range for molecule 1
atomsel: frame -1 out of range for molecule 1
    while executing
"$sel writepdb $outAllAtom"
    (procedure "::cgnetworking::writeAllAtomPdb" line 11)
    invoked from within
"::cgnetworking::writeAllAtomPdb $outAllAtom $inMolId $a_nk "
    (procedure "::cgnetworking::toNetworkingCG" line 273)
    invoked from within
"::cgnetworking::toNetworkingCG $statusProc $inMolId $cgResName $cgPrefix
$outPDB $outAllAtom $outTop $outParm $numBeads $numSteps $epsInit
    (procedure "::cgnetworking::networkCGMolecule" line 14)
    invoked from within
"::cgnetworking::networkCGMolecule ::cggui::addStatusLine
$::cggui::currentToCGMol $::cggui::toCGshapeResName
$::cggui::toCGshapeNamePrefix $::cggu..."
    (procedure "::cggui::buildShapeCGExecute" line 119)
    invoked from within
    invoked from within
".cggui.toCGShapeFrame.applyDB invoke"
    ("uplevel" body line 1)
    invoked from within
"uplevel #0 [list $w invoke]"
    (procedure "tk::ButtonUp" line 24)
    invoked from within
"tk::ButtonUp .cggui.toCGShapeFrame.applyDB
    (command bound to event)

How should I rectify this? Please suggest.


Anirban Ghosh
Grade Based Engineer
SECG, Bioinformatics
C-DAC, Pune

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