VMD-L Mailing List

From: Jane Bailey (jbailey.xtal_at_googlemail.com)
Date: Wed Feb 17 2010 - 11:14:55 CST

Benjamin Bouvier wrote:
> Jane,
>
> Open Applications in finder, right-click VMD and 'show package
> contents'. Browse to Contents/MacOS, right-click startup.command and
> 'get info'. Under the 'open with' tab, select 'Terminal.app' rather
> than 'Smultron.app'...
> Cheers,
>
> Benjamin
>
> On Wed, 17 Feb 2010 16:35:53 +0100, Jane Bailey
> <jbailey.xtal_at_googlemail.com> wrote:
>
>> Dear all,
>>
>> I am a new user of VMD, however I couldn't make it work in my office
>> computer which is Mac osx 10.4.11
>> The version I downloaded is MacOS X OpenGL (Intel x86)
>> <http://www.ks.uiuc.edu/Development/Download/download.cgi?UserID=&AccessCode=&ArchiveID=987>
>> (Apple MacOS-X (10.4.7 or later) with hardware OpenGL (native
>> bundle)). I simply compiled it and copied the program to the
>> Application like for other Mac softwares. But when I double-click the
>> program, it says in Smultron:
>>
>> #!/bin/sh
>>
>> # startup.command
>> # This is the script executed by VMDLauncher to actually start VMD.
>>
>> p=`dirname "$0"`
>> "$p/../Resources/VMD.app/Contents/MacOS/VMD" $*
>>
>>
>> Does anybody have idea what was wrong with my installing?
>>
>> Many thanks!
>> Jane
>
>
Dear Benjamin,

It worked!! But now another problem starts...
I am doing the VMD Tutorials, but none of the state files could be
loaded. Did I miss installing some components?

The terminal reads:

Info) In any publication of scientific results based in part or
Info) completely on the use of the program STRIDE, please reference:
Info) Frishman,D & Argos,P. (1995) Knowledge-based secondary structure
Info) assignment. Proteins: structure, function and genetics, 23, 566-579.
Type 'user add key Control-2 {my VMD commands...}' to use this key
couldn't read file "setss.tcl": no such file or directory
ERROR) Could not read file titin_I1.pdb
Unable to load file 'titin_I1.pdb' using file type 'pdb'.
ERROR) Could not read file titin_z1.pdb
Unable to load file 'titin_z1.pdb' using file type 'pdb'.
ERROR) Could not read file titin_z2.pdb
Unable to load file 'titin_z2.pdb' using file type 'pdb'.
ERROR) Could not read file titin_m5.pdb
Unable to load file 'titin_m5.pdb' using file type 'pdb'.
ERROR) Could not read file titin_I27.pdb
Unable to load file 'titin_I27.pdb' using file type 'pdb'.
invalid command name "vmd_use_pdb_ss"
Illegal molecule specification '1': Could not
find molecule '1'.
Illegal molecule specification '2': Could not
find molecule '2'.
Illegal molecule specification '3': Could not
find molecule '3'.
couldn't read file "setss.tcl": no such file or directory
Couldn't open psf file I27-wat.psf
ERROR) Could not read file I27-wat.psf
Unable to load file 'I27-wat.psf' using file type 'psf'.
dcdplugin) Could not access file 'I27-smd-cv-0.05Aps.dcd'.
ERROR) Could not read file I27-smd-cv-0.05Aps.dcd
Unable to load file 'I27-smd-cv-0.05Aps.dcd' using file type 'dcd'.
invalid command name "waitfor"
Couldn't open psf file z1z2-tlt_wb.psf
ERROR) Could not read file z1z2-tlt_wb.psf
Unable to load file 'z1z2-tlt_wb.psf' using file type 'psf'.
ERROR) Could not read file z1z2-tlt_wb.pdb
Unable to load file 'z1z2-tlt_wb.pdb' using file type 'pdb'.
{{1.000000 0.000000 0.000000 -2.212467} {0.000000 1.000000 0.000000
-0.717593} {0.000000 0.000000 1.000000 -4.596669} {0.000000 0.000000
0.000000 1.000000}} {{-0.063712 0.130975 -0.989337 0.000000} {-0.648723
0.747892 0.140787 0.000000} {0.758357 0.650774 0.037317 0.000000}
{0.000000 0.000000 0.000000 1.000000}} {{0.017453 0.000000 0.000000
0.000000} {0.000000 0.017453 0.000000 0.000000} {0.000000 0.000000
0.017453 0.000000} {0.000000 0.000000 0.000000 1.000000}} {{1.000000
0.000000 0.000000 0.000000} {0.000000 1.000000 0.000000 0.000000}
{0.000000 0.000000 1.000000 0.000000} {0.000000 0.000000 0.000000 1.000000}}
0
0
Unable to change color name

Thanks!

Jane