From: Majid Shahbabaei (m.shahbabaei_at_gmail.com)
Date: Fri Feb 06 2015 - 01:19:13 CST

Dear Josh and users,

Thank you very much for your help. I did follow as you explained (I had to
place the "fi ; \\" expression before "chmod +x run_vmd_tmp ; \\"). But the
following error happened

/usr/local/bin/vmd: 480: exec: /usr/local/lib/vmd/vmd_LINUX: not found

I also tried the Axel's comments at (
http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/16988.html) but
nothing happens. The same error

/usr/local/bin/vmd: 480: exec: /usr/local/lib/vmd/vmd_LINUX: not found

Any comment would be appreciated.

Thanks in advance

MajiD

On Fri, Feb 6, 2015 at 12:13 PM, Josh Vermaas <vermaas2_at_illinois.edu> wrote:

> 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> 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] *On Beh**alf
>> Of *Majid Shahbabaei
>> *Sent:* Thursday, February 05, 2015 12:32 PM
>> *To:* 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
>>
>
>
>