The Molecular Graphics Laboratory Forum

AutoDock, AutoLigand, MGLTools, Vina, PyRx and more.
It is currently Thu Apr 19, 2018 9:18 am

All times are UTC




Post new topic Reply to topic  [ 9 posts ] 
Author Message
PostPosted: Tue Aug 18, 2009 5:10 pm 
Offline
Millimolar User
Millimolar User
User avatar

Joined: Tue Aug 18, 2009 4:18 pm
Posts: 3
Hi:

I am using mac intel os 10.5.7. I copied the script to the tcsh terminal and got the error message after typing in my password.

[Yoshikazu-Takadas-Computer:~] yoshikazutakada% tar xzvf autodock_vina_1_0_2_mac.tar.gz
autodock_vina_1_0_2_mac/
autodock_vina_1_0_2_mac/install.sh
autodock_vina_1_0_2_mac/vina_license.txt
su
./autodock_vina_1_0_2_mac/install.sh
[Yoshikazu-Takadas-Computer:~] yoshikazutakada% su
Password:
su: Sorry

Please advise me on how to solve the problem.
Thank you for your help.


Top
 Profile  
 
PostPosted: Wed Aug 19, 2009 10:20 pm 
Offline
MGL member
MGL member
User avatar

Joined: Mon Oct 20, 2008 9:39 pm
Posts: 202
Hi Yoshikazu,

You shouldn't paste the whole thing at once, because you are supposed to type your root password after "su", when prompted.

_________________
If you don't get your question answered here, consider posting it on the AutoDock mailing list instead of this forum. Please do not email or PM me with requests for help.


Top
 Profile  
 
PostPosted: Thu Aug 20, 2009 4:53 pm 
Offline
Millimolar User
Millimolar User
User avatar

Joined: Tue Aug 18, 2009 4:18 pm
Posts: 3
Thanks. I found that my password was a problem. I needed to register my root password using directory utility. Otherwise "su" command does not work. I will paste how I solved the problem, since other mac users may have the same problem.

I found how to do it here.
http://irrashai.wordpress.com/2008/02/0 ... n-leopard/

How-To: Enable Root Password in Leopard

Thursday, 7 Feb 08 in How-To, Technology
Tags: leopard, mac os x, root password
You got a Mac running on Leopard (probably out of the box). You created your account, add in some personal info, and an admin password. Later in life (8 hours gap), you would open your terminal and simply type “su -” for purposes of i dunno, just root stuff. This reminds you, “Did i ever had one? I don’t recall any root password.” *did i mention this was me?*
Well to let you off the hook (the first 30 seconds in forgetfulness limbo and the next minute in regression), it’s not enabled by default. Here’s how to go about enabling root.

1. Go to: Applications -> Utilities -> Directory Utility
2. (Be sure to click the padlock to allow you to perform edits.)
3. Click Edit -> Enable Root Password
4. Type a new password and retype to confirm.

yoshi


Top
 Profile  
 
PostPosted: Thu Nov 12, 2009 5:06 am 
Offline
Millimolar User
Millimolar User
User avatar

Joined: Wed Nov 11, 2009 10:32 am
Posts: 1
yoshikazu takada wrote:
Thanks. I found that my password was a problem. I needed to register my root password using directory utility. Otherwise "su" command does not work. I will paste how I solved the problem, since other mac users may have the same problem.

I found how to do it here.
http://irrashai.wordpress.com/2008/02/0 ... n-leopard/

How-To: Enable Root Password in Leopard

Thursday, 7 Feb 08 in How-To, Technology
Tags: leopard, mac os x, root password
You got a Mac running on Leopard (probably out of the box). You created your account, add in some personal info, and an admin password. Later in life (8 hours gap), you would open your terminal and simply type “su -” for purposes of i dunno, just root stuff. This reminds you, “Did i ever had one? I don’t recall any root password.” *did i mention this was me?*
Well to let you off the hook (the first 30 seconds in forgetfulness limbo and the next minute in regression), it’s not enabled by default. Here’s how to go about enabling root.

1. Go to: Applications -> Utilities -> Directory Utility
2. (Be sure to click the padlock to allow you to perform edits.)
3. Click Edit -> Enable Root Password
4. Type a new password and retype to confirm.

yoshi


Hello yoshikazu,
I am working on MAC OS and the problem discussed in this forum,the same I was facing before visiting the forum.
I have done all steps given here and I have solved it.

So I just want to thank you for sharing this helpful information.

_________________
grüner tee


Top
 Profile  
 
PostPosted: Mon Nov 16, 2009 6:29 pm 
Offline
Millimolar User
Millimolar User
User avatar

Joined: Mon Nov 16, 2009 4:28 pm
Posts: 2
Hi Yoshi, hi everyone,

I am a new Mac user and I am trying to install Vina on my computer. I am not too savy about computers in general so I am a little in over my head. I am having problems with installing Vina and I was wondering if you guys could help.

First off, when I download Vina, instead of having the file autodock_vina_1_0_2_mac.tar.gz, I just get autodock_vina_1_0_2_mac.tar. I think this means that my computer is unzipping the file automatically. But I don't know how to change this, or how to go about it in the X11 command window. Do you guys have any idea how I can fix this?

Also, I have not been able to change my directory. Would this be because I still haven't properly performed the previous step?

Thank you so much for your help! I can't wait to get vina running!!

Maryam


Top
 Profile  
 
PostPosted: Mon Nov 16, 2009 10:23 pm 
Offline
MGL member
MGL member
User avatar

Joined: Mon Oct 20, 2008 9:39 pm
Posts: 202
If you don't have a root password set up, you can also do

Code:
sudo su

instead of
Code:
su


OR

Code:
sudo ./autodock_vina_1_0_2_mac/install.sh

instead of
Code:
su
./autodock_vina_1_0_2_mac/install.sh

_________________
If you don't get your question answered here, consider posting it on the AutoDock mailing list instead of this forum. Please do not email or PM me with requests for help.


Top
 Profile  
 
PostPosted: Mon Nov 16, 2009 10:29 pm 
Offline
MGL member
MGL member
User avatar

Joined: Mon Oct 20, 2008 9:39 pm
Posts: 202
Maryam wrote:
Hi Yoshi, hi everyone,

I am a new Mac user and I am trying to install Vina on my computer. I am not too savy about computers in general so I am a little in over my head. I am having problems with installing Vina and I was wondering if you guys could help.

First off, when I download Vina, instead of having the file autodock_vina_1_0_2_mac.tar.gz, I just get autodock_vina_1_0_2_mac.tar. I think this means that my computer is unzipping the file automatically.

Use Firefox for downloading, OR use
Code:
tar xvf autodock_vina_1_0_2_mac.tar

instead of
Code:
tar xzvf autodock_vina_1_0_2_mac.tar.gz


Quote:
But I don't know how to change this, or how to go about it in the X11 command window. Do you guys have any idea how I can fix this?

Also, I have not been able to change my directory. Would this be because I still haven't properly performed the previous step?


Yes. Incidentally, Vina does not require X11 (although PMV might) You can install and use it from the Terminal app.

_________________
If you don't get your question answered here, consider posting it on the AutoDock mailing list instead of this forum. Please do not email or PM me with requests for help.


Top
 Profile  
 
PostPosted: Tue Nov 17, 2009 2:29 pm 
Offline
Millimolar User
Millimolar User
User avatar

Joined: Mon Nov 16, 2009 4:28 pm
Posts: 2
Wow thank you so much! I really appreciate your quick response. I went ahead with the installing and I think it worked. I did however run into more issues which I will ask you here if you don't mind. Also, I am not sure if it is ok for me to continue this conversation in this thread or start a new one. If I am in the wrong place, I apologize. But for now, here are my next-step issues:

I managed to install vina (sudo was especially helpful). I got as far as running the program and seeing the Usage summary. However I did notice that at the end of that section, it was written "Missing receptor" and this was followed by "correct usage" and the rest of the information. I can see my receptor pdbqt file in the vina folder so I am not sure why it is telling that the receptor is missing.

Keeping this in mind, I went ahead and tried to run the docking by entering the configuration file (conf.txt), and also tried the typing method. None of them worked (I get command not found, or something similar). But I am also noticing that unlike the tutorial video, the last line (where I am supposed to enter config conf.txt) does not end with "... vina.exe" but rather ends with "$".

Can you tell me what I can do differently to make this work?

Thank you very much.

Maryam


Top
 Profile  
 
PostPosted: Mon Mar 15, 2010 10:19 pm 
Offline
MGL member
MGL member
User avatar

Joined: Mon Oct 20, 2008 9:39 pm
Posts: 202
billyME wrote:
I know that is an old topic, but I have a short question:
Can i update my mac 10.8.2 vina version with leopard version? Are those two compatible?


I don't understand what you are asking, and 10.6 (Snow Leopard) is the latest OS X version, as of this writing. However, please see http://vina.scripps.edu/manual.html#mac and the rest of the manual.

_________________
If you don't get your question answered here, consider posting it on the AutoDock mailing list instead of this forum. Please do not email or PM me with requests for help.


Top
 Profile  
 
Display posts from previous:  Sort by  
Post new topic Reply to topic  [ 9 posts ] 

All times are UTC


Who is online

Users browsing this forum: No registered users and 2 guests


You cannot post new topics in this forum
You cannot reply to topics in this forum
You cannot edit your posts in this forum
You cannot delete your posts in this forum
You cannot post attachments in this forum

Search for:
Jump to:  
POWERED_BY
Translated by Maël Soucaze © 2009 phpBB.fr