VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Fri Jan 08 2010 - 08:27:06 CST

On Fri, 2010-01-08 at 09:48 -0300, Ocar Campos wrote:

> Prahit:
>
> I see you are a newcomer to linux, welcome!... those kind of
> errors are because you are running the comands as a normal user, you
> should be superuser or root to install some softwares that need to

NOOOOOOO!!!!

please don't make people with little experience mess up
their systems by doing everything as superuser. i have been
maintaining application software on several machines and
clusters for years without having to use (or know!!) the
root password.

for installing software that is not part of the standard
operating system software package, it is _much_ better to
first install and test it within the (safe) confines of a
normal user account. there is nothing in VMD that requires
root privilege, so it is perfectly ok to install it into
$HOME/vmd-1.8.7 and the launch script into $HOME/bin
(which on most distributions is already part of the default
path, so it is not even needed to change environment variables).

doing stuff as a superuser is _very_ dangerous. one typo and
the whole machine may become unusable.

> access some kind of files so for installing vmd you must log as root,
> so in console you can write:
>
> su

if you give advice, please make it good. using plain "su" is
a bad idea, too, since it inherits the environment of the previous
user. that can have all kinds unwanted side effects. please always
use "su -" or "su -l" which will clear the environment and give
you a "login shell". if you do stuff as a superuser, you cannot be
paranoid enough.

cheers,
    axel.

> and then push enter, it will ask you the root password which it may be
> different from your user password and then the prompt should say
> something like:
>
> root_at_linux-3qfw:
>
> after this try with the commands I gave you and this should do the
> work...
>
> O'car Campos C.
> Bioinformatics Engineering Student.
> University of Talca.
> Chile.
>
>
> 2010/1/3 Prathit Chatterjee <pc20apr_at_yahoo.co.in>
> Hello Ocar,
> I tried the commands you suggested me and I write to
> you the consequences which I face here.
>
> After I give the command "./configure" after going to the
> vmd-1.8.6 directory using the command cd vmd-1.8.6, the
> following thing occurs which I am pasting below( I just want
> to know whether it is right or wrong):
>
> neelanjana_at_linux-3qfw:~/vmd-1.8.6> ./configure
> using configure.options: LINUXIA64 OPENGL FLTK TK ACTC IMD
> NETCDF TCL PTHREADS SILENT
>
> Then I gave the command "cd src" and then after entering into
> the src directory, I gave the required command as told by you,
> ie. "make install". Then the following error occred which I am
> mentioning you by pasting the exact reply from the linux
> window:
>
> neelanjana_at_linux-3qfw:~/vmd-1.8.6/src> make install
> mkdir: cannot create directory `/usr/local/lib/vmd':
> Permission denied
> mkdir: cannot create directory `/usr/local/lib/vmd':
> Permission denied
> make: *** [install] Error 1
>
> So, I dont know exactly what is the error occuring and thus, I
> need your help. I am pretty much thankful to you for your
> co-operative reply and shall be highly obliged if you grant me
> the favor again amidst your tight schedules.
> Thanking you,
> Prathit Chatterjee
> Junior Resrach Fellow(CSIR)
> under Dr. Neelanjana Sengupta
> Molecular Dynamics Simulations of Biomolecules
> Electronic Structure Theory Group
>
> Centre for Materials Characterization
> National Chemical Laboratory
>
> Pune,411008,India
>
>
>
>
> --- On Sat, 2/1/10, Ocar Campos <ocarnorsk138_at_gmail.com>
> wrote:
>
> From: Ocar Campos <ocarnorsk138_at_gmail.com>
> Subject: Re: vmd-l: vmd installation in linux
> To: "Prathit Chatterjee" <pc20apr_at_yahoo.co.in>, "Vmd
> l" <vmd-l_at_ks.uiuc.edu>
> Date: Saturday, 2 January, 2010, 5:50 PM
>
>
>
> Hello:
>
> I usually do this, it works for archlinux, ubuntu and
> fedora, so it should be the same for opensuse, this is
> all working in a terminal:
>
> 1.- Download VMD.
>
> 2.- Uncompress the tar.gz file, and place yourself in
> the vmd folder, i.e.: cd vmd-1.8.6
>
> 3.- Execute the configuration file: ./configure
>
>
> 4.- Place yourself in the src folder: cd src
> cd src
> 5.- As root execute the make install: make install
>
>
> 6.- if you want to launch vmd from anywhere copy the
> vmd bin to /usr/local/bin then in console write vmd
> and it should launch anywhere.
>
> 7.- if ater copying the file doesn't work writting vmd
> anywhere I think you should add /usr/local/bin to the
> enviroment path.
>
>
> Hope this helps.
>
>
> Cheers.
>
> O'car Campos C.
> Bioinformatics Engineering Student.
> University of Talca.
> Chile.
>
>
> 2010/1/2 John Stone <johns_at_ks.uiuc.edu>
>
> Hi,
> Can you be more specific about what problem
> you're having after you
> install? Any of the recent versions could
> work, but I need to know what
> problem you're experiencing in order to help
> you solve it. What happens
> if you run VMD in text mode via "vmd -dispdev
> text"?
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
>
> On Sat, Jan 02, 2010 at 09:38:09AM +0530,
> Prathit Chatterjee wrote:
> > Hi,
> > can anyone help me installing vmd in
> linux. I have opensuse11.1 software
> > version of linux. Also, I have windows xp
> and I know that it is very
> > simple to install linux in windows but
> linux has other advantages. I tried
> > several versions from the vmd download
> link in my computer and tried to
> > install it by reading the suggestions
> given in the readme file. But, it is
> > not working in the linux. So I want to
> know the exact version of vmd for
> > installing in the linux(opensuse 11.1)
> > Thanking you,
> >
> > Prathit Chatterjee
> > PhD Student
> > Junior Research Fellow(CSIR)
> > Computational Chemistry
> > Electronic Structure Theory Group
> > Under Dr. Neelanjana Sengupta(scientist)
> > Centre for Materials Characterization
> > National Chemical Laboratory
> > Pune,411008
> >
> >
> ----------------------------------------------------------------------
> >
> > The INTERNET now has a personality.
> YOURS! See your Yahoo! Homepage.
>
>
> --
> 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
>
>
>
>
> ______________________________________________________________
>
> The INTERNET now has a personality. YOURS! See your Yahoo!
> Homepage.
> 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com 
Institute for Computational Molecular Science
College of Science and Technology
Temple University, Philadelphia PA, USA.