After installation of VMD, it showed: VMD installation complete. Enjoy!
However when I tried to run it in terminal it shows: > rlwrap: command not found > /usr/local/lib/vmd/vmd_LINUX: command not found. What should I do?
If it said installation complete, it should easily run. Usually you just have to run command "vmd" from terminal and vmd opens up.. what command are you using to run it? "rlwrap not found" is common, but it does not stop vmd from opening..
yeah! I gave the same command "vmd" in terminal and it shows me that error.
You need to edit the /usr/local/bin/vmd file as following
Replace
set vmdprefixcmd="rlwrap -C vmd -c -b(){}[],&^%#;|\\ -f ${MASTERVMDDIR}/vmd_completion.dat "
by
set vmdprefixcmd="rlwrap -C vmd -c -f ${MASTERVMDDIR}/vmd_completion.dat "
and
set vmdprefixcmd="rlwrap -C vmd -c -b(){}[],&^%#;|\\ "
by
set vmdprefixcmd="rlwrap -C vmd -c "
For details see the link
http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/19158.html
Hope it will solve your issue.
I had the same problem yesterday, tried all the fixes mentioned in the forum topic, but the real fix was to switch to English localization. I did it with reinstalling Ubuntu. My guess is that somehow the foreign character tables mix up the vmd install. BTW i had Hungarian Ubuntu set up first, i haven`t tried if it gives the same error with other languages.
Problem in running VMD on Ubuntu.
After installation of VMD, it showed: VMD installation complete. Enjoy!
However when I tried to run it in terminal it shows: > rlwrap: command not found > /usr/local/lib/vmd/vmd_LINUX: command not found. What should I do?
As i said 3 posts earlier, the same problem was solved or me by changing the language of the system. My guess is there is some sort of internationalization problem, and that's why it only effects systems with not English typesets.
I had the same problem in US, and the answer of Himanshu Joshi was really helpful. Thank you very much. Just to find the line with word "rlwrap" in file /usr/local/bin/vmd (for Pico editor it is command Ctrl+W rlwrap) and in the next lines to make changes like Himanshu suggested. Everything works.
I am facing the same problem. I tried the way that Himanshu suggested but it permission is denied each and every time. :(
anyway, i use the language of my system is english.
Have anyone solved this problem /???
Hi Rofiques,
Why don't you edit the file as super user (root), I hope that will fix the permission issues.
Type
sudo su
Press enter and give your password
Next, try to edit the file
https://help.gnome.org/users/gedit/stable/gedit-edit-as-root.html.en
I am also facing the same problem. after installation i got "VMD installation complete. Enjoy!" massage. but while running vmd it shows
Info) VMD for LINUXAMD64, version 1.9.2 (December 29, 2014)
Info) http://www.ks.uiuc.edu/Research/vmd/
Info) Email questions and bug reports to [email protected]
Info) Please include this reference in published work using VMD:
Info) Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual
Info) Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38.
Info) -------------------------------------------------------------
Info) Multithreading available, 12 CPUs detected.
Info) Free system memory: 28334MB (88%)
Info) Dynamically loaded 2 plugins in directory:
Info) /usr/local/lib/vmd/plugins/LINUXAMD64/molfile
vmd >
what could I do ???
I am getting same error
lab@lab-desktop:~$ vmd
/usr/local/lib/vmd/vmd_LINUXAMD64: /usr/lib/x86_64-linux-gnu/mesa/libGL.so.1: no version information available (required by /usr/local/lib/vmd/vmd_LINUXAMD64)
Info) VMD for LINUXAMD64, version 1.9.3 (November 30, 2016)
Info) http://www.ks.uiuc.edu/Research/vmd/
Info) Email questions and bug reports to [email protected]
Info) Please include this reference in published work using VMD:
Info) Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual
Info) Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38.
Info) -------------------------------------------------------------
Info) Multithreading available, 2 CPUs detected.
Info) CPU features: SSE2
Info) Free system memory: 958MB (48%)
Info) No CUDA accelerator devices available.
Warning) Detected X11 'Composite' extension: if incorrect display occurs
Warning) try disabling this X server option. Most OpenGL drivers
Warning) disable stereoscopic display when 'Composite' is enabled.
Info) OpenGL renderer: Mesa DRI Mobile Intel® GM45 Express Chipset
Info) Features: STENCIL MDE CVA MTX NPOT PP PS GLSL(OVF)
Info) Full GLSL rendering mode is available.
Info) Textures: 2-D (8192x8192), 3-D (512x512x512), Multitexture (8)
terminate called after throwing an instance of 'std::runtime_error'
what(): Error. OSPRay only runs on CPUs that support at least SSE4.1.
Aborted (core dumped)
lab@lab-desktop:~$
Further I did below step
You need to edit the /usr/local/bin/vmd file as following
Replace
set vmdprefixcmd="rlwrap -C vmd -c -b(){}[],&^%#;|\\ -f ${MASTERVMDDIR}/vmd_completion.dat "
by
set vmdprefixcmd="rlwrap -C vmd -c -f ${MASTERVMDDIR}/vmd_completion.dat "
and
set vmdprefixcmd="rlwrap -C vmd -c -b(){}[],&^%#;|\\ "
by
set vmdprefixcmd="rlwrap -C vmd -c "
please find attached screen shot
I am new to linux and on understanding, why it is happing?
working solution for me:
cd /usr/local/bin
sudo gedit vmd
Then, I changed first line
#!/bin/csh
to
#!/bin/tcsh
After saved vmd file, the software worked without problem.
Thank you for your reply but, i got another error.
lab@lab-desktop:/$ vmd
bash: /usr/local/bin/vmd: /bin/tcsh: bad interpreter: No such file or directory
lab@lab-desktop:/$
You should install tcsh first.
sudo apt install tcsh
After that,
change to
#!/bin/tcsh (do not remove any sign, please)
I suppose you used original vmd file.
Hello Folks,
The installation problems are mostly due to the graphics libraries and environmental glitches. I found that the older version of vmd works in some cases as a get around. So, you may give a try to download and install the previous/different versions rather than sticking to the latest one.
Dear Folks, I tried all solutions on web. But neither of them worked. I have enough shell script experiment. So I tried sh, csh and tcsh options. Of course your computer should has tcsh shell. There is tcsh shell on my computer because of my older experiment with Boltztrap.
Maybe this page can help you:
http://ubuncent.blogspot.com.tr/2009/02/install-vmd-on-ubuntu_23.html
Somehow, older versions used csh, but new version use tcsh.
Again,
sudo apt install tcsh (if not installed)
cd /usr/local/bin
sudo gedit vmd
Then, I changed first line
#!/bin/csh
to
#!/bin/tcsh
I have tried what Berna Uyanik proposed, but it still does not work.
I also tried changing the code as indicated in
http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/19158.html
defaultvmddir=/usr/local/lib/vmd: Command not found.
vmdbasename=vmd: Command not found.
Missing }.
If someone knows if i can fix this, il be very thankful. I need to run vmd, and i just got into ubuntu.
Thanks
Hi David,
A quick get around, try to install the older version of vmd
and see if it works.
I spent the whole yesterday trying installing all versions and doing the suggested solutions on each version. Well i stopped at version 1.8.6. Y think there arenolders but i gave up.
for Ubuntu 16.04 64bit,
cd vmd-1.9.3/
1) vi configure
# Directory where VMD startup script is installed, should be in users' paths.
$install_bin_dir="/home/jiyo/bin";
# Directory where VMD files and executables are installed
$install_library_dir="/home/jiyo/lib/$install_name";
2)./configure LINUXAMD64
3) cd src
4) make install
5)vmd
come from http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/16988.html
> The README in the vmd-1.8.7 working directory under 'Required Libraries' tells me I require the approriate GL or OpenGL libraries on my system, I wonder whether this is what I don't have, I don't know? What could be the problem, please help.
the problem is, that the bourne shell version of the startup script
that ships with version 1.8.7 has a small issue that makes it incompatible
with your /bin/sh which is a derivative of /bin/ash and not /bin/bash.
there are two workarounds:
a) just edit your vmd launch script to have
#!/bin/bash
as first line.
b) install tcsh or csh and then install vmd again.
that will install the csh version of the launch script
which has been more thoroughly tested.
cheers,
axel.
> Cheers,
> Mike
>
I'v followed all of your suggestion, but there is still problem on my vmd, as this:
root@Precision-5510:/# vmd
/usr/local/lib/vmd/vmd_LINUXAMD64: /usr/lib/x86_64-linux-gnu/mesa/libGL.so.1: no version information available (required by /usr/local/lib/vmd/vmd_LINUXAMD64)
Info) VMD for LINUXAMD64, version 1.9.4a7 (July 12, 2017)
Info) http://www.ks.uiuc.edu/Research/vmd/
Info) Email questions and bug reports to [email protected]
Info) Please include this reference in published work using VMD:
Info) Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual
Info) Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38.
Info) -------------------------------------------------------------
Info) Multithreading available, 8 CPUs detected.
Info) CPU features: SSE2 AVX AVX2 FMA
Info) Free system memory: 29GB (93%)
Info) No CUDA accelerator devices available.
Warning) Detected X11 'Composite' extension: if incorrect display occurs
Warning) try disabling this X server option. Most OpenGL drivers
Warning) disable stereoscopic display when 'Composite' is enabled.
Info) OpenGL renderer: Mesa DRI Intel(R) HD Graphics 530 (Skylake GT2)
Info) Features: STENCIL MSAA(4) MDE CVA MTX NPOT PP PS GLSL(OVFS)
Info) Full GLSL rendering mode is available.
Info) Textures: 2-D (16384x16384), 3-D (512x512x512), Multitexture (8)
rlwrap: warning: vmd killed by SIGSEGV (core dumped).
rlwrap has not crashed, but for transparency,
it will now kill itself with the same signal
Segmentation fault (core dumped)
Wish your answers, Thanks!
Hi everybody,
There are many ways to solve the occurred errors with the installation of VMD tool on Ubuntu operating system. Herein, I mentioned some useful ways to eliminate your problem without spending more much time to search in the internet for finding keys to open your lock!
1) check your system to know which version of Ubuntu installed on your system. Based on its status (64 or 32) you should try to download VMD software from the developer website. To know more information about your system please run the following command in your linux terminal:
2) cat /etc/issue or uname -a
After this step, you should go to VMD website to download the latest version of this software.
3) open your terminal and then run the following command
sudo apt-get update
***** enter your pass.
sudo apt-get upgrade
sudo apt-get install
sudo apt-get install csh
After these steps, your terminal is ready to install VMD. Next, check VMD website to find convenience version of this tool for your device. Then, you should install the downloaded package in your system root. So, in your terminal you should type:
>~$ sudo -s
This command usher you to where the fact is!. Then you should create a folder named software in this path to copy your downloaded package here. For creating a folder, you should run the following command:
>~# mkdir software
now your folder has created and you should copy VMD from Downloads folder inside the new path via the following command:
>~# cp Downloads/vmd-1.9.3.bin.LINUXAMD64-CUDA8-OptiX4-OSPRay111p1.opengl.tar /software/
After this step, the time has come to unzip your file. Then, you should run the following command:
>~# tar xvf vmd-1.9.3.bin.LINUXAMD64-CUDA8-OptiX4-OSPRay111p1.opengl.tar
and in the next steps, you should run the following commands one after another :
cd vmd-1.9.3.
./configure
In this step you should see the following line in your terminal:
using configure.options: LINUXAMD64 OPENGL OPENGLPBUFFER FLTK TK ACTC CUDA IMD LIBSBALL XINERAMA XINPUT LIBOPTIX LIBOSPRAY LIBTACHYON VRPN NETCDF COLVARS TCL PYTHON PTHREADS NUMPY SILENT ICC
Then, copy the bold text and run the following command:
./configure LINUXAMD64 OPENGL OPENGLPBUFFER FLTK TK ACTC CUDA IMD LIBSBALL XINERAMA XINPUT LIBOPTIX LIBOSPRAY LIBTACHYON VRPN NETCDF COLVARS TCL PYTHON PTHREADS NUMPY SILENT ICC
After the aforementioned step, you should run the following command in your terminal:
cd src/
After entering this path, the final step of VMD installation should be performed through the following command:
/src# make install
And for this moment you should see the following message:
Make sure /usr/local/bin/vmd is in your path.
VMD installation complete. Enjoy!
Okay! you get victory and the VMD installed on your system. To examine the efficacy of your VMD installation process, you should type "exit" in your terminal to close your root pass and then type "vmd" in your terminal. The vmd tool will be opened for you!
Have happy time with your project.
Kind regards
Hassan
Use the follow:
sudo su
apt-get install tcsh
vi /usr/local/bin/vmd
Change csh for tcsh and save.
You can install VMD with this way:
1.download vmd :Https://www.ks.uiuc.edu/Research/vmd-1.9.3
2.open "Download Vmd 1.9.3 for macOsx...." Then "Linux_64openGl,CUDA,OSPRay,..."
Click on version1.9.3(2016-11-30)
3.creat account with your email then start to download with click on "continue with registration".
4.When download was finished, open your terminal and type "gksudo nautilus" then create new file on your "computer" (your computer root),copy your vmd file on your new folder and extract vmd.
5.Then type "sudo -s" appear ~# symbol in your terminal.Then type "cd /vmd-1.9.3" and type ./configure
6.type "cd src" on your terminal and type "make install".
VMD installation complete. Enjoy.
Close terminal and open again type "vmd" ,VMD opened.
I was facing the problem with ubuntu 19.10 version
I actually intalled
1. tcsh
sudo apt install tcsh
2. installed vmd 1.9.3 having plugins in the same directory as the vmd directory.
./configure LINUXAMD64
3. cd src
4. sudo make install
5. Restart the terminal
and
6. typed vmd
it just run without any problem.
I have installed Ubuntu 20.04 on my windows 10. I want to run the VMD software in it, but I am unable to do so. can anyone please guide me how to open the VMD window after I have accessed its folder via Ubuntu?
Hi. I'm a newbie in Linux and VMD too. But I've installed Ubuntu 20.04 and VMD-1.9.4a43 by myself, so I hope I can help this case little bit.
When I was doing rbcg-tutorial by UIUC, I faced a problem.
What I've done : try to run vmd -dispdev text -e 01-coarse-grain.tcl > 01-coarse-grain.log
The problem I got : (/lib/x86_64-linux-gnu/libGL.so.1: no version information available)
After I tried what you guys have been suggested, I gave up. Because I still face that problem. So, what I can do is to take another route.
1. Open VMD by typing "vmd" on terminal with the sample's directory
2. Open Extensions ----> Tk Console
3. Type this : "source 01-coarse-grain.tcl"
4. The vmd will be closed, but you will get the result. What I want is the cg with .pdb, so it doesn't matter if I'm not get the 01-coarse-grain.log.
Hope it will help.
I am getting this problem
bash: /home/nkeot/Desktop/new_vmd/vmd-1.9.4a51/bin: Is a directory.
can anyone help me
Niharika Keot: press ctrl+H in home and find bashrc. open bashrc and type
/home/nkeot/Desktop/new_vmd/vmd-1.9.4a51/bin
bottom the page.
remove all vmd then install again by downloading this tar file https://www.ks.uiuc.edu/Development/Download/download.cgi?UserID=&AccessCode=&ArchiveID=1475
sudo apt-get update
sudo apt-get upgrade
./configure
cd src
make install
vmd
i get this when trying to configure VMD on Linux
"VMD plugin directory not found.
Please compile the VMD plugins and do 'make distrib' to copy them
into a 'plugins' directory linked or located in this directory.
Be sure your PLUGINDIR environment variable is set before running
'make distrib' in the plugin build area."
To install and run VMD on Ubuntu OS you can use the following protocol
Preparing system
Update and upgrade your system before installing VMD. Open a terminal by pressing Ctrl+Alt+T and paste the following commands.
$ sudo apt-get update
$ sudo apt-get upgrade
Downloading VMD
Go to this page and select an appropriate VMD version compatible with your system. To download VMD, you will have to register using your university email address. After successful registration, it will automatically start downloading. Here, we are downloading VMD 1.9.3, not the latest alpha version as it is a test version, therefore, you might face some issues.
Installing VMD
Go to the directory where you have downloaded the tar file and extract. Let’s say we have downloaded this file in the Downloads directory.
$ cd Downloads/
$ tar xvzf vmd-1.9.3.bin.LINUXAMD64-CUDA102-OptiX650-OSPRay185.opengl.tar.gz
It will create a new directory, namely, vmd-1.9.3.
Move inside this new directory and install as shown below.
$ cd vmd-1.9.3/
Now, open the file configure and change the $install_bin_dir and $install_library_dir if you wish otherwise leave the default values as it is. Now paste the following command.
$ ./configure
Now, move inside the src directory to install.
$ cd src/
$ sudo make install
It will take a moment to finish the installation. Now, you can type vmd in the terminal and it should work. However, sometimes, it does not work that way. You have to add it to the path. For that, follow the steps given below.
$ sudo nano ~/.bashrc
Go to the end of the file and paste the following:
$ /path/to/vmd
For example, $ /usr/local/bin/vmd
Save and exit.
$ source ~/.bashrc
If it still doesn’t open then add the following path instead of the above.
$ /usr/local/bin/vmd/vmd_LINUXAMD64
$ source ~/.bashrc
Now, it should work properly.
Thank you the help. i am still having same problem. i think has has something to do with the plugins directory
My mistake is coming from this point
"Now, open the file configure and change the $install_bin_dir and $install_library_dir if you wish otherwise leave the default values as it is. Now paste the following command."
For Error. OSPRay only runs on CPUs that support at least SSE4.1.
I simply used gedit on the generated vmd file in the
/usr/local/bin folder ($sudo gedit vmd) and included the
following lines
in the file:
if $?VMDNOOSPRAY == "0")
then setenv VVMDNOOSPRAY off endif
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