My question is:
Has anyone been able to use autodock tools?
How to by pass this bug?
Has autodock tools been retired?
I am still studying how to preform docking simulations. I think i just use autodock tools to generate the .pdbqt files from .pdb file correct? is there a way to do that without using autodock tools?
Are there other programs that have better support? or the community prefers to use other software than AutoDock?
You could try installing the module explicity: python -m pip install oldnumeric - though one would expect that the installation should have handled all the necessary installations, so this probably won't work. AutoDock Vina is popular, but I don't know whether that's different from, superceding, or part of AutoDock Tools.
The problem is AutoDockTools needs an older version of Numpy, which had a module oldnumeric but dropped it from Numpy 1.9.0. The bug tracker mentions pip install numpy==1.8.2, but the person reporting the bug stated it doesn't solve the issue.
I tried python -m pip install oldnumeric but it seems there is no oldnumeric library in pip, I get this error message:
Could not find a version that satisfies the requirement oldnumeric (from versions: ) No matching distribution found for oldnumeric
AutoDockTools is used only to prepare the receptor and ligand files in preparation for docking by Autodock-Vina (this is from my reading so far since I cannot install the program and learn better), which is why one of my questions was: if there is a way to generate the correct receptor and ligand .pdbqt files from their .pdb files without using AutoDockTools.
I don't HAVE to use AutoDock, I just want to preform docking simulations for my project. Which is why my final question was if there are other tools that are better supported than AutoDock? Something that the academic community finds more reliable?
Uninstall the broken Ubuntu version, then download and install from the software developer:
How to Download AutoDockTools:
After you have clicked on this AutoDockTools link, you will be taken to our lab's "MGLTools Web Portal" downloads page.
Download the latest version of MGLTools: If you are running on Linux, Mac OS X, SGI, or Windows, we recommend you download the Binary
distribution.
Follow the instruction provide on the website to install AutoDockTools.
.pdbqt is a protein file format that support in the AutoDock software. The main purpose of using AutoDock is to doing Docking Analysis instead of convert pdb file to pdbqt file. If you only want to do the file conversion, openBabel is one of the options.
Last time I used Windows GUI to run. I am not sure about the error, maybe u can try to navigate to your AutoDock installation path and run the command with the version number again.
You could try installing the module explicity:
python -m pip install oldnumeric- though one would expect that the installation should have handled all the necessary installations, so this probably won't work. AutoDock Vina is popular, but I don't know whether that's different from, superceding, or part of AutoDock Tools.The problem is AutoDockTools needs an older version of Numpy, which had a module oldnumeric but dropped it from Numpy 1.9.0. The bug tracker mentions
pip install numpy==1.8.2, but the person reporting the bug stated it doesn't solve the issue.Thanks jrj.healey for your replay,
I tried
python -m pip install oldnumericbut it seems there is no oldnumeric library in pip, I get this error message:Could not find a version that satisfies the requirement oldnumeric (from versions: ) No matching distribution found for oldnumericAutoDockTools is used only to prepare the receptor and ligand files in preparation for docking by Autodock-Vina (this is from my reading so far since I cannot install the program and learn better), which is why one of my questions was: if there is a way to generate the correct receptor and ligand .pdbqt files from their .pdb files without using AutoDockTools.
I don't HAVE to use AutoDock, I just want to preform docking simulations for my project. Which is why my final question was if there are other tools that are better supported than AutoDock? Something that the academic community finds more reliable?
Thank you