From: Aravind Ravichandran (
Date: Wed Jun 27 2018 - 05:26:18 CDT

Dear VMD users,
  I am doing PCA analysis in VMD 1.9.3 (Linux version- I am using centos
7) using NMWIz extension, and using default parameters. I am able to
perform ANM and GNM calculation and I am getting the following error
only with PCA. I am not understanding what the error is about to solve
it. Can anyone help me with this?

@> Superposing [ 0%] 3s

@> Superposing [ 0%] 2s

@> Superposing [ 1%] 2s


@> Superposing [100%] 0s
    while executing
"exec $::NMWiz::pybin $::NMWiz::prody {*}$args"
    (procedure "::NMWiz::prodySubmitPCAjob" line 61)
    invoked from within
    (procedure "::NMWiz::prodySubmitJob" line 26)
    invoked from within
    invoked from within
".nmwizprody.submitFrame.prodySubmit invoke"
    ("uplevel" body line 1)
    invoked from within
"uplevel #0 [list $w invoke]"
    (procedure "tk::ButtonUp" line 22)
    invoked from within
"tk::ButtonUp .nmwizprody.submitFrame.prodySubmit"
    (command bound to event)

I saw the same error being mentioned in the Prody GitHUb page, but

Thank you in advance for the reply.

Aravind R
Junior Research Fellow,
Ranabir Das Lab,
National Centre for Biological sciences,
Banglore, India