Autodock takes the input form only in .pdbqt. This format is accepted in no other software. How to prepare the ligand in AutoDock Tools? When i prepare the ligands in other software and import it in ADT, the hydrogens and double bonds are lost.
Thanks.
Hi Rajiv,
You don't have to use ADT. Try Open Babel.
http://openbabel.org/wiki/Main_Page
http://openbabel.org/wiki/Category:Installation
Dear Rajiv,
I use to prepare ligands using UCSF Chimera. It is a free-of-charge and easy software. It can be used for both preparing ligands/proteins and visualizing results.
Rajiv Lakkaniga
check our new software AMDock available for Ubuntu and Windows
https://github.com/Valdes-Tresanco-MS/AMDock
https://github.com/Valdes-Tresanco-MS/AMDock-win
AMDock (Assisted Molecular Docking) is a user-friendly graphical tool to assist in the docking of protein-ligand complexes using Autodock-Vina or AutoDock4. This tool integrates several external programs for processing docking input files, define the search space (box) and perform docking under user’s supervision.
http://autodock.scripps.edu/faqs-help/how-to/how-to-prepare-a-ligand-file-for-autodock4/?searchterm=pdb%20to%20pdbqt
PyRx does ligand preparation and virtual screening. It is easy to use and free software.
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