VMD-L Mailing List
From: John Stone (johns_at_ks.uiuc.edu)
Date: Sun Mar 25 2018 - 11:52:48 CDT
- Next message: Denish Poudyal: "i thought I could run a 100 ns NAMD simulation in my laptop for a protein-hormone system containing around 2000 atoms in its pdb file(4lnx.pdb). But even to run a simulation for four hundred fifty thousand steps, it has taken almost 4700 minutes. is this normal or its low? the device has 4 cores with 16 gigs of ram and 4 gigs of gpu(amd). Or any suggestions to run it faster???"
- Previous message: Francesco Pietra: "Fwd: Fwd: ParseFEP for restating FEP"
- In reply to: SM Bargeen A Turzo: "Regarding Installation of DruGui"
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Hi,
What happens if you run VMD in text mode (preventing the extensions
menu script from being run) via -dispdev text and then load the druigui
package manually like this:
package require drugui
Do you get any more specific errors other than the failed load?
I would suggest contacting the drugui developers since there may
be some non-obvious dependency on a compiled shared library or
something else that might cause this if you don't get a more
informative error message after following my suggestion above.
Best,
John Stone
vmd_at_ks.uiuc.edu
On Sat, Mar 24, 2018 at 04:23:04AM +0000, SM Bargeen A Turzo wrote:
> Hi all,
>
> Very new to VMD and I have been trying to install DruGui, following the
> instructions on DruGui site. However, VMD is not installing the plugin and
> giving me the following error:
>
> Info) -------------------------------------------------------------
> Info) Multithreading available, 4 CPUs detected.
> Info) OpenGL renderer: Intel(R) Iris(TM) Graphics 6100
> Info) Features: STENCIL MDE MTX NPOT PP PS GLSL(OVF)
> Info) Full GLSL rendering mode is available.
> Info) Textures: 2-D (16384x16384), 3-D (2048x2048x2048), Multitexture
> (8)
> Info) Dynamically loaded 2 plugins in directory:
> Info) /Users/smturzo/Desktop/dev/vmd/VMD
> 1.9.3.app/Contents/vmd/plugins/MACOSXX86/molfile
> The drugui package could not be loaded:
>
> ---------------------------------------------------------------------------
>
> Additional information:
>
> Python version: Python 2.7.14
>
> Numpy version: 1.12.1
>
> I have also added the plugin installation line in loadplugins.tcl in line
> 186 as shown here:
>
> ### Modeling menu
> vmd_install_extension autoionizegui autoigui "Modeling/Add Ions"
> autoionize
> vmd_install_extension solvate solvategui "Modeling/Add Solvation
> Box"
> vmd_install_extension autopsf autopsf_tk_cb "Modeling/Automatic PSF
> Builder"
> vmd_install_extension cggui cggui_tk "Modeling/CG Builder"
> vmd_install_extension dowser_gui dowser_tk_cb "Modeling/Dowser"
> vmd_install_extension drugui drugui_tk "Modeling/drugui"
> vmd_install_extension chirality_gui chirality_tk_cb "Modeling/Fix
> Chirality Errors"
> vmd_install_extension cispeptide_gui cispeptide_tk_cb "Modeling/Fix Cis
> Peptide Bonds"
> vmd_install_extension forcefieldtoolkit fftk "Modeling/Force Field
> Toolkit"
> vmd_install_extension inorganicbuilder inorganicBuilder_tk
> "Modeling/Inorganic Builder"
> vmd_install_extension mdff_gui mdffgui_tk "Modeling/MDFF"
> vmd_install_extension membrane membrane_tk "Modeling/Membrane
> Builder"
> vmd_install_extension mergestructs mergestructs_tk "Modeling/Merge
> Structures"
> vmd_install_extension molefacture molefacture_tk "Modeling/Molefacture"
> vmd_install_extension mutator mutator_tk "Modeling/Mutate Residue"
> vmd_install_extension nanotube nanotube_tk "Modeling/Nanotube
> Builder"
> vmd_install_extension torsionplot torsionplot_tk "Modeling/TorsionPlot"
>
> ---------------------------------------------------------------------------
>
> Any help will be greatly appreciated.
>
> -Bargeen
-- 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/
- Next message: Denish Poudyal: "i thought I could run a 100 ns NAMD simulation in my laptop for a protein-hormone system containing around 2000 atoms in its pdb file(4lnx.pdb). But even to run a simulation for four hundred fifty thousand steps, it has taken almost 4700 minutes. is this normal or its low? the device has 4 cores with 16 gigs of ram and 4 gigs of gpu(amd). Or any suggestions to run it faster???"
- Previous message: Francesco Pietra: "Fwd: Fwd: ParseFEP for restating FEP"
- In reply to: SM Bargeen A Turzo: "Regarding Installation of DruGui"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]