From: Ivan Gregoretti (ivangreg_at_gmail.com)
Date: Thu Jul 31 2014 - 07:49:34 CDT

Addendum

Also, in my system I can execute the command

ls -gG /usr/local/lib/vmd

and in response I get

-rw-r--r--. 1 2013 Mar 6 09:01 Announcement
drwxr-xr-x. 2 4096 Jan 30 14:42 doc
-rwxr-xr-x. 1 449632 Jun 9 2011 libcudart.so.4
-rwxr-xr-x. 1 143336 Mar 1 2011 libexpat.so.0
-rwxr-xr-x. 1 131599 Feb 29 2012 libhdf5_hl.so.7
-rwxr-xr-x. 1 2963577 Feb 29 2012 libhdf5.so.7
-rwxr-xr-x. 1 7605784 Feb 29 2012 libprotobuf.so.7
-rwxr-xr-x. 1 652249 Mar 5 2011 libsqlite3.so.0
-rw-r--r--. 1 7753 Mar 6 09:01 LICENSE
drwxr-xr-x. 5 4096 Oct 24 2013 plugins
-rw-r--r--. 1 10566 Mar 6 09:01 README
drwxr-xr-x. 8 4096 Oct 24 2013 scripts
drwxr-xr-x. 3 4096 Oct 24 2013 shaders
-rwxr-xr-x. 1 160424 Mar 6 09:01 stride_LINUXAMD64
-rwxr-xr-x. 1 2184618 Mar 6 09:01 surf_LINUXAMD64
-rwxr-xr-x. 1 206344 Mar 6 09:01 tachyon_LINUXAMD64
-rw-r--r--. 1 3166 Mar 6 09:01 vmd_completion.dat
-rwxr-xr-x. 1 14963816 Mar 6 09:01 vmd_LINUXAMD64

You should see something very similar if your "confire" file was
properly edited.

Cheers,

Ivan

Ivan Gregoretti, PhD
Bioinformatics

On Thu, Jul 31, 2014 at 8:31 AM, Ivan Gregoretti <ivangreg_at_gmail.com> wrote:
> Hi Kshatresh,
>
> There seems to be a configuration problem. Two hints to that:
>
> 1) "Tk startup error" and
> 2) being unable to find "/usr/local/lib/vmd/scripts/
> vmd/vmdinit.tcl"
>
> Now, towards solving the problem
>
> Here
> http://www.ks.uiuc.edu/Research/vmd/current/ig/node6.html
> it says that for linux you need to edit the "configure" file that came
> with the VMD tar archive.
>
> For instance, in my Fedora box, this is an excerpt of my "configure" file
>
> ...
> # Directory where VMD startup script is installed, should be in users' paths.
> $install_bin_dir="/usr/local/bin";
>
> # Directory where VMD files and executables are installed
> $install_library_dir="/usr/local/lib/$install_name";
> ...
>
> In my system (which works fine) I can do:
>
> ls vmd-1.9.2a35
> Announcement configure.options doc LINUXAMD64 proteins scripts
> bin data lib msvc python shaders
> configure distrib LICENSE plugins README src
>
> and also the vmdinit.tcl can be found:
>
> stat /usr/local/lib/vmd/scripts/vmd/vmdinit.tcl
> File: ‘/usr/local/lib/vmd/scripts/vmd/vmdinit.tcl’
> Size: 11567 Blocks: 24 IO Block: 4096 regular file
> Device: fd01h/64769d Inode: 2103623 Links: 1
> Access: (0644/-rw-r--r--) Uid: ( 1000/igregore) Gid: ( 1000/igregore)
> Context: unconfined_u:object_r:lib_t:s0
> Access: 2014-07-31 08:22:43.396699329 -0400
> Modify: 2011-04-12 21:40:15.000000000 -0400
> Change: 2014-03-06 09:01:29.882829327 -0500
> Birth: -
>
> Is that how your system is configured and responding? Does proper
> editing of your "configure" file solve the problem?
>
> I hope this helps.
>
> Ivan
>
>
>
> Ivan Gregoretti, PhD
> Bioinformatics
>
>
>
>
> On Thu, Jul 31, 2014 at 6:56 AM, Kshatresh Dutta Dubey
> <kshatresh_at_gmail.com> wrote:
>> Dear Users ,
>>
>> I have installed vmd 1.9.1 on centos 7.0. It is showing several error
>> during start up in vmd shell and some of the features like extension is
>> missing. Following is the log of vmd start:
>> Info) VMD for LINUXAMD64, version 1.9.1 (February 1, 2012)
>> Info) http://www.ks.uiuc.edu/Research/vmd/
>> Info) Email questions and bug reports to vmd_at_ks.uiuc.edu
>> Info) Please include this reference in published work using VMD:
>> Info) Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual
>> Info) Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38.
>> Info) -------------------------------------------------------------
>> Info) Multithreading available, 12 CPUs detected.
>> Info) Free system memory: 29679MB (92%)
>> Info) Creating CUDA device pool and initializing hardware...
>> CUDA error: invalid device symbol, CUDAClearDevice.cu line 62
>> Info) Detected 1 available CUDA accelerator:
>> Info) [0] GeForce GTX 680 8 SM_3.0 @ 1.14 GHz, 2.0GB RAM, KTO, OIO, ZCP
>> Warning) Detected X11 'Composite' extension: if incorrect display occurs
>> Warning) try disabling this optional X server feature.
>> Info) OpenGL renderer: GeForce GTX 680/PCIe/SSE2
>> Info) Features: STENCIL MSAA(16) MDE CVA MTX NPOT PP PS GLSL(OVFGS)
>> Info) Full GLSL rendering mode is available.
>> Info) Textures: 2-D (16384x16384), 3-D (2048x2048x2048), Multitexture (4)
>> ERROR) Tk startup error: this isn't a Tk applicationunknown color name
>> "BACKGROUND"
>> ERROR) Could not read the vmd initialization file -
>> ERROR) source {/usr/local/lib/vmd/scripts/vmd/vmdinit.tcl}
>> ERROR) can't invoke "wm" command: application has been destroyed
>> ERROR) The VMDDIR environment variable is set by the startup
>> ERROR) script and should point to the top of the VMD hierarchy.
>> ERROR) VMD will continue with limited functionality.
>> ERROR) invalid command name "vmd_load_extension_packages"
>>
>> Please help me to solve this issue. Thanks in advance.
>> --
>>
>> Regards
>> Kshatresh
>>