Answer for How to prepare multiple ligands for virtual screening?
If you are screening thousands of compounds, I would suggest you to…
Answer for How to know which database to download for virtual screening?
Hi, You can download the ZINC database of small molecules for virtual…
Answer for How to download compounds for virtual screening?
Please visit the following link: https://bioinformaticsreview.com/20200720/how-to-download-small-molecules-for-virtual-screening-from-zinc-database/
Answer for addition-of-atom-type-in-autodock-vina
Perform force field optimization of your ligand in Vina. Vina uses amber…
Answer for addition-of-atom-type-in-autodock-vina
Why are you docking using Vina? If you have prepared your files…
Answer for unable-to-open-autodock-from-the-ubuntu-terminal-using-aliases
This error means that either python is not installed on your system…
Answer for the atoms in the protein are not same as the atoms in the ligand. the maps are created for the atoms in the protein and error showing is can't find the map for an atom which is not in the protein like can't find cl.map while autodocking
Hi, look for your map file whether it is present in the…
Answer for Problem in launching AutoDock Tools from Ubuntu terminal
Hi Rhea,Since you are a beginner, you can start learning some basic…
Answer for Addition of atom type in AutoDock Vina
At what step are you getting this error? I guess while preparing…
Answer for Error while installing mgltools.
Download the correct file, either mgltools_i86Linux2_1.5.6.tar.gz or mgltools_x86_64Linux2_1.5.6.tar.gz and use the following commands…
Answer for Unable to run Autodock using “adt” alias.
You need to install the Tkinter using the following command: $ sudo apt-get…
Answer for Error in running Autodock Vina from the terminal.
You need to install the x86_64 version of mgl tools (mgltools_x86_64Linux2_1.5.6.tar.gz). This…
Answer for How should I use the “pmv” or “adt”?
"pmv" and "adt" are aliases, not commands, these are used to shorten…
Answer for Problem in moving Autogrid and Autodock
This error is probably arising because you need not use 'sudo' in…
Answer for Problem launching AutoDock Tools from Ubuntu terminal
First of all, make sure your PATH variable has not messed up.…
Answer for Error while trying to open Autodock tools
It seems like you lack tk-dev on your system which is not…
Answer for error-in-running-autodock-vina-adt-mgltools-on-linux
Hi Nithya, Try installing this version (http://mgltools.scripps.edu/downloads/downloads/tars/releases/REL1.5.6/mgltools_x86_64Linux2_1.5.6.tar.gz). The version you…
Answer for MOLECULAR DOCKING
Well, common factors which affect the biological activity of a compound are…
Answer for Why do we choose only one chain of protein for docking?
The chains are removed from the protein structure just to avoid the…