There are a lot of comments regarding MGL Tools / AutoDock Tools not working on Mac. As of Mac Catalina, 32-bit apps such as Autodock Tools and MGL Tools are no longer supported. Creating a virtual machine with a compatible operating system is an alternative which will allow you to install ADT and MGL Tools. This can be done using a tools such as virtual box.
@@SoukRassek.podcast @brown lab pleeeeease reply to this I have the same issue Update: I bought a subscription to Parallels desktop and MGLtools works just fine on it
Thanks a lot for the video, brother! Can you post a quick one on how to run a docking? I have all the programs installed, but the only video tutorials are for Windows. You're the only Mac I've found... Thanks!
This video is one of the most informative and useful video on youtube. Thank you very much for posting it. Id possible please upload some videos about docking in autodock and Schrodinger.
I downloaded and installed MGLTools but then when I open from the application in finder, I see that they are crossed out and error message pops up saying "“AutoDockTools-1.5.6” needs to be updated". How to get over this? Please help!!
@@suisuilover Yeah, it was a tough one. I was really agitated with the issue, and I basically started opening all of the folders, subfolders of the package, and finally, on a terminal file, I was able to open up the program. However, the application folder for this still showed same response. And now I have that terminal file in my shortcut to directly use the program.
Bipasana Shakya I read some reference about this, the key of this problem may be that the mgltools is a 32bit app, however new macos just run 64bit app
I installed all correctly, however, the MGLtool does not work on my MAC as it says it needs update. Can someone help me? I cannot create virtual machine.
Please help huhuhu!!! I'm in the part where pip should be installed but I don't think I downloaded it correctly I followed all the instructions but this is what I got: Traceback (most recent call last): File "/usr/local/bin/pip", line 9, in load_entry_point('pip==21.0.1', 'console_scripts', 'pip')() File "/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/pkg_resources/__init__.py", line 565, in load_entry_point return get_distribution(dist).load_entry_point(group, name) File "/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/pkg_resources/__init__.py", line 2697, in load_entry_point return ep.load() File "/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/pkg_resources/__init__.py", line 2370, in load return self.resolve() File "/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/pkg_resources/__init__.py", line 2376, in resolve module = __import__(self.module_name, fromlist=['__name__'], level=0) File "/Library/Python/2.7/site-packages/pip-21.0.1-py2.7.egg/pip/_internal/cli/main.py", line 60 sys.stderr.write(f"ERROR: {exc}") ^ SyntaxError: invalid syntax Virgels-MacBook-Air:~ vctorres1$ sudo easy_install pip Searching for pip Best match: pip 21.0.1 Processing pip-21.0.1-py2.7.egg pip 21.0.1 is already the active version in easy-install.pth Installing pip script to /usr/local/bin Installing pip2.7 script to /usr/local/bin Installing pip2 script to /usr/local/bin Using /Library/Python/2.7/site-packages/pip-21.0.1-py2.7.egg Processing dependencies for pip Finished processing dependencies for pip Virgels-MacBook-Air:~ vctorres1$ pip Traceback (most recent call last): File "/usr/local/bin/pip", line 9, in load_entry_point('pip==21.0.1', 'console_scripts', 'pip')() File "/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/pkg_resources/__init__.py", line 565, in load_entry_point return get_distribution(dist).load_entry_point(group, name) File "/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/pkg_resources/__init__.py", line 2697, in load_entry_point return ep.load() File "/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/pkg_resources/__init__.py", line 2370, in load return self.resolve() File "/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/pkg_resources/__init__.py", line 2376, in resolve module = __import__(self.module_name, fromlist=['__name__'], level=0) File "/Library/Python/2.7/site-packages/pip-21.0.1-py2.7.egg/pip/_internal/cli/main.py", line 60 sys.stderr.write(f"ERROR: {exc}") ^ SyntaxError: invalid syntax Virgels-MacBook-Air:~ vctorres1$
I've downloaded the Autodock, when I tried to open it it says "AutoDockTools-1.5.6 need to be updated" may I know is there any solution to this problem? I really need help with this~
@@vernonvest5104 I think I concluded that ADT wasn’t compatible with my mac. I used ADT through virtual box instead. It worked for the docking that I needed to complete but then it crashed later on due to storage issues. I would recommend it as a short term solution!
@@aulanempouli6149 oh i see, im using the M1 which and unfortunately virtual box cant run 😵😵 do you know any alternative for ADT? Im new to bioinformatics
Hello! Can you help me with Biovia discovery studio visualiser download in Mac? I can see its download links for windows and linux but can't seem to find a link for MacBook!
Hi! I am having problems with Mac OS Catalina, when I attempt to open the MGT tools it says the app is not compatible. Any idea on how to fix it? I successfully installed Xquartz but the message about "Installer" wanting access to control "system events" never popped up... I don't know it this has anything to do with it. Please help!
Hi there ! Thanks for this nice and informative tutorial .. I have a problem with MGL tools, I installed it several times and I couldn't find it in apps .. What should I do ?
Hello. This is an amazing informative video. Been searching for it since a long time. Thanks A LOT. I still have some confusions about directories though. Can you please guide me regarding it because I saved the folders just like you tell in the end of video but don't know how to dock from Mac now? I'm stuck regarding using terminals. Can you please talk on skype or email? Please reply. Really need your help. It would be extremely helpful. Please. Thank you.
i just want Baudock vina to do ligand docking screening but i guess i need MGL tools too. Is there a way to install MGL tools for macOS Catalina (64 bit)? I've installed vina but can't open anything with it. i need the MGL tools right? or PyRx ?
Hello, thank you for the video! I see that when you open ADT, you got an error related to "/usr/X11/lib/libGL.1.dylib" and grid parameters. How did you solve this? I'm getting the same error and, therefore, cannot run any docking. Thank you.
Hello. Your tutorial videos are some! just safe me from a lot of problems. moreover you have any idea on how to install AutodockVina in macOS Catalina? Thanks a lot!
I'm trying to run autodock vina using chimera on my mac and it keeps failing to run. I'm using a 64bit installation for Catalina. Any advice on what to do?
@@tanvikhokhawat1341 yes, I don’t remember exactly what I did but I had to reconfigure the shell on my laptop. You can see at about 7:14 that he’s got bash. I had something else so had to look up how to change that. Hope that helps!
There are a lot of comments regarding MGL Tools / AutoDock Tools not working on Mac. As of Mac Catalina, 32-bit apps such as Autodock Tools and MGL Tools are no longer supported. Creating a virtual machine with a compatible operating system is an alternative which will allow you to install ADT and MGL Tools. This can be done using a tools such as virtual box.
Hi, my mac has an M1 chip and cannot run virtualbox, is there still a way i could run MGL tools without it ?
@@SoukRassek.podcast @brown lab pleeeeease reply to this I have the same issue
Update: I bought a subscription to Parallels desktop and MGLtools works just fine on it
Can you make a tutorial for this too? I request, it because I have tried it myself and haven't succeeded
Thanks a lot for the video, brother! Can you post a quick one on how to run a docking? I have all the programs installed, but the only video tutorials are for Windows. You're the only Mac I've found... Thanks!
very helpful for users with limited knowledge in linux. I am literally installing the programs along with your video. thanks a bunch
This video is one of the most informative and useful video on youtube. Thank you very much for posting it. Id possible please upload some videos about docking in autodock and Schrodinger.
I downloaded and installed MGLTools but then when I open from the application in finder, I see that they are crossed out and error message pops up saying "“AutoDockTools-1.5.6” needs to be updated". How to get over this? Please help!!
me too, have u solve this problem?
@@suisuilover Yeah, it was a tough one. I was really agitated with the issue, and I basically started opening all of the folders, subfolders of the package, and finally, on a terminal file, I was able to open up the program. However, the application folder for this still showed same response. And now I have that terminal file in my shortcut to directly use the program.
Bipasana Shakya I read some reference about this, the key of this problem may be that the mgltools is a 32bit app, however new macos just run 64bit app
this is because we i updated our mac to the new version
did it work with you ?
THIS IS THE BEST GUIDE!!! MUCH GRATITUDE TO YOU!! MORE POWER & BLESSINGS!!
I installed all correctly, however, the MGLtool does not work on my MAC as it says it needs update. Can someone help me? I cannot create virtual machine.
Thanks for your super helpful vdo. I have a problem about PIP. It says " couldn't find index page for "pip". (maybe misspelled?). Any suggestion?
please how can i get autodock tools to work in MacOS 11 Big Sur ?
Could you teach for docking by using open-babel on mac please >
Please help huhuhu!!! I'm in the part where pip should be installed but I don't think I downloaded it correctly
I followed all the instructions but this is what I got:
Traceback (most recent call last):
File "/usr/local/bin/pip", line 9, in
load_entry_point('pip==21.0.1', 'console_scripts', 'pip')()
File "/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/pkg_resources/__init__.py", line 565, in load_entry_point
return get_distribution(dist).load_entry_point(group, name)
File "/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/pkg_resources/__init__.py", line 2697, in load_entry_point
return ep.load()
File "/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/pkg_resources/__init__.py", line 2370, in load
return self.resolve()
File "/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/pkg_resources/__init__.py", line 2376, in resolve
module = __import__(self.module_name, fromlist=['__name__'], level=0)
File "/Library/Python/2.7/site-packages/pip-21.0.1-py2.7.egg/pip/_internal/cli/main.py", line 60
sys.stderr.write(f"ERROR: {exc}")
^
SyntaxError: invalid syntax
Virgels-MacBook-Air:~ vctorres1$ sudo easy_install pip
Searching for pip
Best match: pip 21.0.1
Processing pip-21.0.1-py2.7.egg
pip 21.0.1 is already the active version in easy-install.pth
Installing pip script to /usr/local/bin
Installing pip2.7 script to /usr/local/bin
Installing pip2 script to /usr/local/bin
Using /Library/Python/2.7/site-packages/pip-21.0.1-py2.7.egg
Processing dependencies for pip
Finished processing dependencies for pip
Virgels-MacBook-Air:~ vctorres1$ pip
Traceback (most recent call last):
File "/usr/local/bin/pip", line 9, in
load_entry_point('pip==21.0.1', 'console_scripts', 'pip')()
File "/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/pkg_resources/__init__.py", line 565, in load_entry_point
return get_distribution(dist).load_entry_point(group, name)
File "/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/pkg_resources/__init__.py", line 2697, in load_entry_point
return ep.load()
File "/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/pkg_resources/__init__.py", line 2370, in load
return self.resolve()
File "/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/pkg_resources/__init__.py", line 2376, in resolve
module = __import__(self.module_name, fromlist=['__name__'], level=0)
File "/Library/Python/2.7/site-packages/pip-21.0.1-py2.7.egg/pip/_internal/cli/main.py", line 60
sys.stderr.write(f"ERROR: {exc}")
^
SyntaxError: invalid syntax
Virgels-MacBook-Air:~ vctorres1$
I've downloaded the Autodock, when I tried to open it it says "AutoDockTools-1.5.6 need to be updated" may I know is there any solution to this problem? I really need help with this~
Same problem here!!
@@aulanempouli6149 did u solve this problem?
@@vernonvest5104 I think I concluded that ADT wasn’t compatible with my mac. I used ADT through virtual box instead. It worked for the docking that I needed to complete but then it crashed later on due to storage issues. I would recommend it as a short term solution!
@@aulanempouli6149 oh i see, im using the M1 which and unfortunately virtual box cant run 😵😵 do you know any alternative for ADT? Im new to bioinformatics
@@vernonvest5104 Unfortunately i do not, so sorry
Thanks a lot buddy :)
Hello! Can you help me with Biovia discovery studio visualiser download in Mac? I can see its download links for windows and linux but can't seem to find a link for MacBook!
same 😭
indeed the best video
Hi! I am having problems with Mac OS Catalina, when I attempt to open the MGT tools it says the app is not compatible. Any idea on how to fix it? I successfully installed Xquartz but the message about "Installer" wanting access to control "system events" never popped up... I don't know it this has anything to do with it. Please help!
I am having the same problem....
me too
SAME HERE.
When I open the Autodock tool, it shows that the software needs to be updated. Could you help with this error message?
Could anybody tell me how to install Autodock tools in Mac? It says some upgrade OS TO Catalina. Could anyone tell me about it?
can u please post a video for pyrx and biovia discovery studio
Hi there !
Thanks for this nice and informative tutorial .. I have a problem with MGL tools, I installed it several times and I couldn't find it in apps .. What should I do ?
Look in your applications in your files, not your launchpad. I couldn't find it in my launchpad either but found it there.
Hello. This is an amazing informative video. Been searching for it since a long time. Thanks A LOT. I still have some confusions about directories though. Can you please guide me regarding it because I saved the folders just like you tell in the end of video but don't know how to dock from Mac now? I'm stuck regarding using terminals. Can you please talk on skype or email? Please reply. Really need your help. It would be extremely helpful. Please. Thank you.
This article may help you on navigating directories! www.macworld.com/article/2042378/master-the-command-line-navigating-files-and-folders.html
This was really helpful. Thanks!
i just want Baudock vina to do ligand docking screening but i guess i need MGL tools too. Is there a way to install MGL tools for macOS Catalina (64 bit)? I've installed vina but can't open anything with it. i need the MGL tools right? or PyRx ?
Thank you for the tutorial. How do you download the latest version of MGM tools 1.5.7 (ccsb.scripps.edu/mgltools/downloads/)?
thank you for such a wonderful video and please upload one protein-ligand docking tuturial on Macbook
how can I update the Autodocking as it is not open after I updated my MAC
mgltools can’t run well in macOS catalina, you need to degradation your MacOS to 10.14, or you can use a virtualbox to install macOS Mojave
Thank you so much! This video was really informative and I was able to install Autodock easily.
Thank you Brown Lab, made installation easy
My download option is not show
I can't go to mgltools.scripts.edu. That shows me "Service Temporarily Unavailable". Is there another way to install MGLTools?
@@Brown_Lab Thanks!! I overlooked it. Sorry for being late to reply to you. This video really helps me.
Hello, thank you for the video! I see that when you open ADT, you got an error related to "/usr/X11/lib/libGL.1.dylib" and grid parameters. How did you solve this? I'm getting the same error and, therefore, cannot run any docking. Thank you.
Not sure for that particular error, may be worth while to check the FAQ and help page for ADT autodock.scripps.edu/faqs-help
Hello. Your tutorial videos are some! just safe me from a lot of problems. moreover you have any idea on how to install AutodockVina in macOS Catalina? Thanks a lot!
Hi! you fix this problem? I do not know how to install VirtualBox in macOS Catalina 😭
Incredibly helpful. Thank you!
Hey. Can you help me with the commands to input to run the autodock vina in the terminal
When in your vina folder that contains the vina program and all the files you need, use ./vina --config ("your config text file")
I'm trying to run autodock vina using chimera on my mac and it keeps failing to run. I'm using a 64bit installation for Catalina. Any advice on what to do?
same for me too! were you able to solve this problem?
@@tanvikhokhawat1341 yes, I don’t remember exactly what I did but I had to reconfigure the shell on my laptop. You can see at about 7:14 that he’s got bash. I had something else so had to look up how to change that. Hope that helps!
Does this program work for M1 MacBook?
Any updates on the m1? Can it be downloaded?