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Questions tagged [autodock]

Questions about the software AutoDock.

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4 votes
1 answer
408 views

Blind docking and targeted docking

I used Autodock Vina and UCSF Chimera to perform blind and targeted docking on a protein from the RCSB database and a molecule I had optimized with Gaussian software.The results are as follows: The ...
sarra6's user avatar
  • 579
4 votes
0 answers
92 views

Are there any open-source or free softwares for covalent docking of multiple ligands?

I am currently screening more than 2000 compounds virtually on Vina, but I would like to perform covalent docking. Unfortunately, Vina's functionality is limited as its requires manual designation of ...
biryaniboi's user avatar
2 votes
0 answers
53 views

How to add Samarium atom type in Autodock Vina? [closed]

While trying to perform docking of a protein containing Samarium atom using Autodock-vina in Ubuntu, the following error arises. "ATOM syntax incorrect: "Sm" is not a valid AutoDock ...
Madhusmita's user avatar
3 votes
0 answers
432 views

How to add atom types in Autodock Vina [closed]

The following problem arises when I use Vina for virtual screening. Vina seems to have only one calculation program, so how do I add the required atomic force field parameters? "ATOM syntax ...
user19894668's user avatar
2 votes
0 answers
683 views

Autodock prepare_receptor4.py script gives error while converting pdb files to pdbqt files [closed]

Cross-posted on Chemistry.SE. I am trying to make pdbqt files from pdb files for Docking with Autodock vina but getting errors while running the prepare_receptor4.py script present in the mgltools ...
user3765252's user avatar
5 votes
2 answers
2k views

How can I get Vina to recognise boron atoms?

I am trying to dock a ligand that features a boron (B) atom. AutoDock Vina throws an error with the following message: ATOM syntax incorrect: "B" is not a valid AutoDock type. Note that ...
Shredderroy's user avatar
10 votes
1 answer
241 views

Are there good tutorials that explain how to use experimental data to customise the force field in AMDock Vina?

I am not a chemist, but I know how to use AMDock to predict the binding affinity of a small molecule to a protein. There is a particular target for which AMDock Vina, with its default force fields, ...
Shredderroy's user avatar
4 votes
1 answer
157 views

Procedure to validate glide docking without a reference ligand on Autodock vina

How can I perform a score-in-place procedure with autodock to validate ma glide docking? It is a new software for me and I don't Know how to use it and how to proceed. Thanks in advance for help.
Giu's user avatar
  • 477