VMD-L Mailing List

From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Thu Feb 05 2015 - 21:13:34 CST

Hi Majid,

Change the configuration file. Ubuntu's (and probably all debian
derivatives) have a version of rlwrap that don't play nice with csh.
VMD's installer, in its infinite wisdom, thinks that if you have a csh
interpreter, you probably want to use it (you don't). There are lines
towards the end of the configuration file that tell it to install a csh
launch script, rather than a sh one (which is the one we want).

This is what I always put in its place:
     -\$(COPY) ../data/.vmdrc ../data/.vmdsensors
./data/vmd_completion.dat "$install_library_dir"
     \$(CD) $vmd_bin_dir ; \\
     if [ -f run_vmd_tmp ]; then \$(DELETE) run_vmd_tmp; fi ; \\
         \$(ECHO) "Info: /bin/csh shell not found, installing Bourne
shell startup script instead" ; \\
         \$(ECHO) '#!/bin/sh' >> run_vmd_tmp ; \\
         \$(ECHO) 'defaultvmddir="$install_library_dir"' >> run_vmd_tmp ; \\
         \$(ECHO) 'vmdbasename=vmd' >> run_vmd_tmp ; \\
         cat $vmd_bin_sh >> run_vmd_tmp ; \\
     chmod +x run_vmd_tmp ; \\
     \$(COPY) run_vmd_tmp "$install_bin_dir"/$install_name ; \\
     \$(DELETE) run_vmd_tmp

My advice is to use search to find the first and last lines from what I
copied over and replace what is in between with the "correct" version
and reinstall (starting with the ./configure step).

-Josh Vermaas

On 02/05/2015 07:55 PM, Majid Shahbabaei wrote:
> Dear Khoung, Norman and VMD users,
>
> Thank you very much for your helps. With your comments I could
> uninstall and install the vmd 1.9.1 and 1.9.2, respectively. After
> installation,it showed the following message
> echo "VMD installation complete. Enjoy!"
> VMD installation complete. Enjoy!
>
> But when I want to run the vmd 1.9.2 the following error occurs.
>
> rlwrap: Command not found.
> /usr/local/lib/vmd/vmd_LINUX: Command not found.
>
> I have seen roughly same problem at
> (http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/19004.html,
> http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/19158.html) and
> tried to follow it but it does not approach anything.
>
> rlwrap: Command not found.
> /usr/local/lib/vmd/vmd_LINUX: Command not found.
>
> Could you please tell me how can I fix it up?
>
> Thanks in advance
>
> MajiD
> On Thu, Feb 5, 2015 at 9:46 PM, Norman Geist
> <norman.geist_at_uni-greifswald.de
> <mailto:norman.geist_at_uni-greifswald.de>> wrote:
>
> Hey,
>
> vmd consists of more than only the startup script located in
> /usr/bin. So to completely remove the old one, which isn’t really
> necessary, you’d need to
>
> rm /usr/bin/vmd; #not VMD
>
> rm -r /usr/local/lib/vmd*; #or similar
>
> To install you might need to be root for the “make install” only,
> as normal users may not write to /usr.
>
> so:
>
> untar
>
> change to vmd dir
>
> ./configure
>
> cd src
>
> sudo make install
>
> Norman Geist.
>
> *From:*owner-vmd-l_at_ks.uiuc.edu <mailto:owner-vmd-l_at_ks.uiuc.edu>
> [mailto:owner-vmd-l_at_ks.uiuc.edu <mailto:owner-vmd-l_at_ks.uiuc.edu>]
> *On Beh**alf Of *Majid Shahbabaei
> *Sent:* Thursday, February 05, 2015 12:32 PM
> *To:* vmd-l_at_ks.uiuc.edu <mailto:vmd-l_at_ks.uiuc.edu>
> *Subject:* vmd-l: Problem by removing vmd 1.9.1 and installing 1.9.2.
>
> Dear all,
>
> I already installed the vmd 1.9.1 on ubuntu 12.04. Now I would
> like to install the vmd 1.9.2. I used the following commands to
> uninstall the 1.9.1.
>
> 1. $ /usr/local/bin
>
> 2. rm VMD
>
> I installed the vmd 1.9.2 by the following commands
>
> 1. untar vmd1.9.2-linuxamd64-opengl.tar.gz
>
> 2. su
>
> 3. ./configure LINUX
>
> 4. exit
>
> 5. cd src
>
> 6. sudo make install
>
> After that I evoked vmd, surprisingly found that the vmd 1.9.1 is
> opened.
>
> I would be appreciated if anybody help me to figure it out.
>
> Thanks in advance
>
>
> MajiD
>
>