VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Jul 03 2018 - 11:46:14 CDT

Hi,
  The error is occuring during the call NMWiz makes to launch the
PCA analysis via ProDy:
    vmdcon -info "Executing: $::NMWiz::pybin $::NMWiz::prody $args"
    set status [exec $::NMWiz::pybin $::NMWiz::prody {*}$args]

Based on that, I would expect that the source of your problem is
that something is wrong with the Python interpreter or ProDy scripts
as installed on your machine. What are $::NMWiz::pybin and $::NMWiz::prody
set to on your machine? Can you run them by hand? Did you try
running the same command that NMWiz tried but running by hand?

Best,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Jun 27, 2018 at 03:56:18PM +0530, Aravind Ravichandran wrote:
> 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
> "::NMWiz::prodySubmitPCAjob"
> (procedure "::NMWiz::prodySubmitJob" line 26)
> invoked from within
> "::NMWiz::prodySubmitJob"
> 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
> unanswered.
>
> Thank you in advance for the reply.
>
> Regards,
> Aravind R
> Junior Research Fellow,
> Ranabir Das Lab,
> National Centre for Biological sciences,
> Banglore, India
> 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/