Comments (13)
@alchymy does this help? https://github.com/forlilab/tutorials/tree/main/installation-mac#vina-executable
from autodock-vina.
macBook is same as yours with Monterey 12.7.4 Download just shows as a Kind 'Document'
It shows as "Document" to me too. It should still work in Terminal. Mac displays it as a "Document" likely because it doesn't have a specified extension. You could change the icon (appearance) and its Type by adding the extension .dylib
if you want to make it a Unix Executable to Mac. But it won't affect the content/nature/function of the script
ps. This isn't a necessary step to run vina. The only change after Mac recognizes the file type is now we could launch Terminal (and a dry run with no options or variable specification, will print only the help message) by double-clicking the executable in Finder. The type of files was not actually changed, but the default way to open it now becomes Terminal, if this is something you wanted to :>
from autodock-vina.
Have now got Vina running with some sample pdbqt format data from the source code "basic_docking/data" on Windows 11 and macOS. There are also sample files in the Scripps ADFR reducing tutorial. Autodock Vina 1.1.2 is also available as an integrated extension to "SAMSON 2023 R1 (macOS)" which seems to be able to take MOL and PDB files and pass the data in the correct format to Vina to process - this app has a GUI interface.
from autodock-vina.
Hi @alchymy
It runs for me on macOS Monterey and my model is MacBook Pro (Retina, 15", Mid 2015).
What is your model and OS?
from autodock-vina.
iMac 27" Intel 2019 running Sonoma 14.4 Will check on my macBook as well.
from autodock-vina.
iMac shows it as a "Kind - Script Editor Document" when downloaded.
from autodock-vina.
macBook is same as yours with Monterey 12.7.4 Download just shows as a Kind 'Document'
from autodock-vina.
The original 1.1.2 vina from scripps downloads appeared as an executable file, did have to "chmod +x vina" to get it to run from a script which passes the parameters to it, but it works and appeared as correct file type when downloaded.
from autodock-vina.
the windows .exe version downloaded as is works fine in a bat file. Will check the above solution.
from autodock-vina.
Yes adding the dylib extension and "./vina_1.2.5_mac_x86_64.dylib" in the .command script works. Many thanks.
from autodock-vina.
@alchymy if you don't add .dylib
extension and you execute ./vina_1.2.5_mac_x86_64
what does it print?
from autodock-vina.
If I take .dylib off again it still runs now. Have got it reading a config file.
My issue now is getting the receptor / ligand file format from mol / pdb to pdbqt format. The suggested ADFR tools don't work in macOS now, Windows version installs but starts then just exits. This is on Windows 11 so not sure if it still runs.
from autodock-vina.
Hi @alchymy
If they're command line tools, it's normal to start and just exit. To not exit instantly, run them in a pre-opened terminal instead of starting from Finder. Adding or changing the extension may change how his file is opened by default but again this shouldn't be a necessary thing. I regret making that comment ><!
Check out the Meeko project for ligand and receptor preparation based on Python libraries:
https://github.com/forlilab/Meeko
If ADFR is preferred, having a Ubuntu VM on Mac will be helpful. See the following notes I left to my fellow students, to use ADT/ADFR on Mac with Apple Silicon (skip the Rosetta parts if yours is Intel)
https://rwxayheee.github.io/ADFR-Suite-and-ADT-in-Ubuntu-VM-on-Apple-Silicon
See this official guide on using ADFR on Win10 through WSL:
https://ccsb.scripps.edu/adcp/windows10/
from autodock-vina.
Related Issues (20)
- Python bindings vina v.s vina executable HOT 13
- Details on scoring function terms HOT 3
- Autogrid4 Atom Type Error with Large Ligand Database HOT 6
- An internal error occurred in ../../../src/lib/parse_pdbqt.cpp(69). HOT 3
- Autogrid4 raise error "dyld: Library not loaded:" HOT 8
- Enormous free energy of binding HOT 6
- Weird protein split in flexible docking HOT 7
- Is AutoDock-Vina applicable to peptides? HOT 3
- Docking to zinc atoms in a non-3,1 tetrahedral conformation HOT 4
- Vina flexible docking HOT 4
- PyPi suggests windwos compatibility of python bindings.
- rdkit.six not found HOT 1
- Problems with Binary installation HOT 1
- Autogrid4 Unknown receptor type: HOT 1
- Vina runtime error: The ligand is outside the grid box HOT 1
- I am getting this error while doing flexible autodock docking HOT 1
- H-bond term HOT 2
- Flexible docking tutorial : no HD map file after autogrid4 HOT 1
- Differences between `*_rigid.pdbqt` and `*.pdbqt` files of receptors HOT 2
- Issue : An internal error occurred in ../../../src/lib/tree.h(101) HOT 3
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from autodock-vina.