VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Feb 17 2010 - 11:55:01 CST

Hi,
  When you work through the tutorials, you need to make sure that
you actually change the working directory before you load the
saved state files, as they assume the structure files and trajectories
are located in the current directory. (use the "cd" command...)

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Feb 17, 2010 at 06:14:55PM +0100, Jane Bailey wrote:
> 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
>
> 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078