Why does my ligand pdbqt is not being found by the auto dock vina?

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Does AMBER or CHARMM force field parameters have coarsed grained side chain parameters?

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Where can I read the force field parameters of amino acids and protein ?

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For mineral / compound characterization studies like FTIR, SEM, XRD, how many replicates should be taken for data analysis?

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What is the reference for the partial charges values for peptides shown in avagadro?

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How to compute the Backward kinematics ?

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How to plot the following XYZ coordinate file?

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How to calculate Ligand-active site distance in a ligand-protein complex from MD simulation?

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What are the potential shell well and atomic solvation parameters for the boron atom?

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How long does it take to design and validate transition state analogue inhibitors?

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How to check if the PMF profile obtained from ABF simulation is correct?

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Ligands with 3,4,5-trihydroxyphenyl group?

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How to Remove different version of atom from pdb Crystal Structure for Docking Preparation?

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How do you get around this AutoDock Vina error?

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The dimensionality of protein and ligand is reduced after docking?

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Best tool to build missing residues, minimize and validate a ligand model?

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Annemarie Honegger

Check where your file is located in your file system compared to the default file path used by your autodock installation and that they are no spelling mistakes in your filenames/command files

Rezi Riadhi Syahdi

Please provide more context or screenshot of your problem. Is it not being found by the Vina environment? or by the Vina searching module?

Thilothamai Jegani Kannan

Rezi Riadhi Syahdi I'm getting the error " error: ligand" in the command prompt i have given the proper path and coding too. is there any chance that my ligand is not properly sequenced or its location path is not defined? i cross-checked with a colleague even then there was the same error

I am sorry I could not apprehend the problem. But one solution I can advise you can use AutoDock Vina integrated in PyRx (Go to their website by google "pyrx sourceforge". In my case, it works pretty well, and there is a free option too that will be perfect for you to try. Please check it out.

Rezi Riadhi Syahdi sure thank you