It is flexible docking

@ but in pyrx i think it’s rigid docking. Is that right?

Thank you for your kind words! 😊 Regarding your question: After opening the ligand in ADT and selecting it under Ligand → Input, it's normal for some hydrogens to disappear because ADT recalculates and adjusts them for proper docking. You don't need to manually add them back. When you prepare the ligand for docking, ADT will automatically add polar hydrogens as needed. Let me know if you have any more questions! 😊

Hello @patelpoonam2884, The issue with 2D structure generation in Discovery Studio might be due to ligand fragmentation. Here are some tips: Ensure the ligand is properly prepared as a single fragment before docking. Verify the docking output file in tools like PyMOL or Chimera to confirm the ligand structure. Check Discovery Studio settings for ligand recognition or try importing receptor and ligand separately. Use alternatives like LigPlot+ or PoseView for 2D interactions if needed. Let me know if you need further help! 😊

Hi @ravenleannearma7320! The error usually means the vina.exe file isn’t in your system’s PATH or the command prompt isn’t in the correct directory. To fix it: Run the command from the folder containing vina.exe (use cd to navigate). Add the folder to your system’s PATH so you can run vina from anywhere. Double-check your command for typos. Let me know if you need more help. Good luck with your thesis! 😊

Thanks for your kind words

Hi @annieonate2306, thank you for your comment! I’m sorry to hear you're having trouble getting the same results. Could you let me know more about the issue? For example: Are you using the same input files and parameters as shown in the tutorial? Are there any specific error messages or unusual outputs in the command prompt? Are you using the same version of AutoDock Vina as mentioned in the video? Feel free to share more details so I can help troubleshoot the problem! 😊

Thanks for your kind words.

You're welcome! If the macromolecules in your protein structure are not part of the binding site or relevant to the docking process, it's a good practice to remove them. This helps focus the docking calculations on the actual binding interactions between the ligand and the protein. However, if those macromolecules are crucial for maintaining the protein's structural integrity or are involved in the binding site, you might need to keep them. It ultimately depends on the specifics of your study. Let me know if you need further clarification! 😊

You're welcome!

Hi @shalinimuthu98! If you don’t see the AutoDock Vina option, ensure Vina is installed, and check Chimera’s preferences to link the Vina executable. Also, make sure you’re using a compatible Chimera version. Check the video description for helpful links. Let me know if you need more help!

You are welcome

Yes, similar steps can be applied for Scopus data as well. Once you extract the data from Scopus, you’ll need to filter and clean it for bibliometric analysis, just like with Dimensions.ai. However, the specific process might vary slightly depending on the format of the exported data and the tools you are using. Let me know if you’d like a detailed guide for Scopus! 😊

If PubChem doesn't have the structure available, you can create it using tools like ChemDraw. After drawing the 2D structure in ChemDraw, you can convert it to a 3D structure using Chem3D, which is often bundled with ChemDraw. Alternatively, you can use software like Avogadro to manually build the molecule and optimize its geometry. Once you have the 3D structure, save it in a compatible format (e.g., PDB or MOL2) for molecular docking. Tools like Open Babel can help convert file formats if needed. Let me know if you need more guidance! 😊

Hi @AmardeepKumar-z7x! To dock ruthenium complexes: Prepare Complex: Use tools like Chimera or Avogadro to build and optimize the geometry. Parameterize Metal: Generate force field parameters for ruthenium using tools like Antechamber or quantum chemistry software. Docking: AutoDock Vina may have limitations with metals. Consider specialized software like GOLD for better handling. Let me know if you’d like a detailed guide! 😊

The "memory leak of type 'BHtree'" error is related to Python bindings but usually doesn't stop docking. To fix this: Ensure you're using the latest versions of AutoDock Vina and Python (Python 3.7/3.8 is recommended). Check your input files and parameters for errors. Run the terminal as Administrator if on Windows. If the issue persists, try reinstalling Vina or running it in a clean environment. Let me know if you need further help! 😊

The "memory leak of type 'BHtree'" error is related to Python bindings but usually doesn't stop docking. To fix this: Ensure you're using the latest versions of AutoDock Vina and Python (Python 3.7/3.8 is recommended). Check your input files and parameters for errors. Run the terminal as Administrator if on Windows. If the issue persists, try reinstalling Vina or running it in a clean environment. Let me know if you need further help! 😊

Hi @thomaskrajeev5608! The config.txt file isn’t included in the default downloads; it’s a file you need to create yourself to set the docking parameters. In the tutorial, I explain how to write it step by step. Here’s the basic format for the config.txt file: receptor = receptor.pdbqt ligand = ligand.pdbqt center_x = 0 center_y = 0 center_z = 0 size_x = 20 size_y = 20 size_z = 20 exhaustiveness = 8 your command might look like this: vina --config config.txt --out output.pdbqt

You can't directly dock with a 2D SDF image in PyRx. However, you can convert the 2D SDF file from PubChem into a 3D structure using tools like Open Babel or PyRx itself for energy minimization. This 3D structure is required for docking.

It seems like the interface you're using might not be configured correctly or is invoking a Python Shell due to a missing file or path issue. Ensure you've installed AutoDockTools properly, and double-check that the Python path is correctly set. If the problem persists, try reinstalling AutoDockTools or running it as an administrator. Let me know if you need more help!

@@Axonist Thank you so much for your help, I reinstalled the AutoDockTools and now it is working.

@@chanikarkare727 sounds great...Excellent

Hello @tasnimnajihah1139, docking scores can vary due to differences in parameters, input files, or system settings. Ensure that: The protein and ligand are prepared correctly (e.g., charges, protonation states). The grid box dimensions and center match the tutorial. The same version of AutoDock Vina is used. If everything checks out, slight variations are normal, but significant differences may require revisiting the setup. Let me know if you need further help!

Thank you for your suggestion! Unfortunately, creating a WhatsApp group is not feasible at the moment. However, you are more than welcome to ask your queries here in the KZbin comment section, and I’ll do my best to assist you.

​@@Axonist Sure

Thank you for your comment! You can search "dimensions.ai" on Google Scholar to find several published papers related to bibliometric analysis. Based on your field of expertise, you can choose any of them that fits your needs. For the analysis, you can use tools like Excel, Python with suitable libraries, or R-based software such as Bibliometrix or Biblioshiny. Additionally, Java-based tools like CiteSpace or VOSviewer are great options-it’s all up to your preference! Let me know if you need further guidance.

You're right-PDB format doesn’t retain charges assigned during Dock Prep in Chimera. To fix this, save the receptor in MOL2 format after Dock Prep, as it includes charges. Then, use OpenBabel to convert the MOL2 file to PDBQT for PyRx compatibility. This ensures the charges are preserved.

Discovery Studio allows detailed visualization of Van der Waals interactions in docked complexes. Load your structure, use the Analyze Ligand Interactions tool, and view the 2D/3D Interaction Diagram to identify and analyze these forces.

"Hi @neelam5100! To create a config.txt file, open a text editor (like Notepad), and add the necessary parameters: receptor, ligand, center_x, center_y, center_z, and size_x, size_y, size_z. Save the file as config.txt in the same folder as your docking files. Let me know if you need more help!"

Hi @neelam If you're not seeing the grid option to save in PDBQT format, make sure you’ve correctly set up the grid box in AutoDock Tools. Sometimes, you need to select the macromolecule and set the grid parameters before the option appears. Let me know if that helps!

Google Scholar is generally not recommended for bibliometric analysis due to several limitations, such as inconsistent citation data, lack of transparency, and issues with data reliability. For accurate and comprehensive results, it’s better to use sources like Scopus or Web of Science.

@@Axonist Thank you sir.

@@surendrajagwan9236 You are most welcome dear

Thanks for the feedback! All the links and files are already provided in the description box! Let me know if you have any trouble accessing them.

I m not Dr. H. Ismail. Although Thanks for your kind suggestion. I will try to publish a new video on md Simulation via gromacs including all parameters analysis.

Thanks for your kind suggestion. I will try to share a video on x score software very soon. Thanks again

Thanks for your kind words

Thanks for your kind words..

You can try the following steps: Ensure the folder you're pasting into has the necessary permissions. Right-click the folder, select "Properties," go to the "Security" tab, and ensure your user has "Write" access. Run the file explorer as an administrator and try pasting again.

Thank you so much for your kind words

You can identify the ligand (like quercetin) based on prior research, literature, or experimental data showing its interaction with the protein. PubChem helps you find its structure, but the ligand-protein pairing usually comes from known studies or hypothesis-driven docking.

Scopus and Web of Science aren't freely accessible, but if you've reviewed a research article for Elsevier, you can get 30 days of free access to Scopus and ScienceDirect. You can then export the data for use in VOSviewer or Biblioshiny. PubMed data, however, can't be directly used in VOSviewer without some conversion.

Hello, I am facing the same problem. Did you get it resolved?

Thanks a lot 😊 for your kind words

The zero-charge error usually means some atoms are missing charges. Try these steps: Check the PDB file for proper atom definitions. Add Hydrogens using tools like AutoDockTools. Assign Charges manually in AutoDockTools. Give these a try and see if it resolves the issue!

The reference creation part involves collecting relevant academic papers and then organizing them based on citation counts, co-authorships, or keywords. If you didn’t catch that part, you might want to check the section where I explained how to extract data from Scopus or Web of Science. If you still need help, let me know!"

To identify ligands in predicted structures, you can look for the small molecule or compound that interacts with the protein or receptor in the docking results. In AutoDock Vina, the ligand is typically the smaller, non-protein structure within the binding site of the larger protein structure. You can visualize this using molecular visualization tools like PyMOL or Chimera, which will allow you to clearly see how and where the ligand is binding to the target protein.

Thanks for your question! If you're not analyzing data based on affiliation or corresponding author, there's no need to fill in the missing details. Otherwise, it's best to do so. For other types of analysis, VOSviewer shouldn't create any issues.

@@Axonist can you tell me which all analysis are done using corresponding author data in Vosviewer? Can i do the following tests without complete corresponding author data: Co-authorship (Unit of analysis: authors); Citation (Unit of analysis: authors); Bibliographic coupling (Unit of analysis: authors); Co-citation (Unit of analysis: cited authors)?

@@uncletom11000 You can perform the analyses you mentioned in VOSviewer even with incomplete corresponding author data, but there are trade-offs: Co-authorship: Possible missing connections, leading to underrepresentation of collaborations. Citation: You might miss some citations, so results could be less comprehensive. Bibliographic coupling: Reduced strength of connections due to missing shared references. Co-citation: Generally more resilient, but complete data is always better for accuracy. In short, while possible, incomplete data may impact the reliability of your results.

Thanks for your kind suggestion

Yes, you can manually add the three articles to the CSV file for your bibliometric analysis. Make sure to fill in key columns like Title, Authors, Publication Year, Journal Name, and DOI. If available, include Abstract and any other relevant columns. Once added, you can proceed with your analysis as usual.

@@Axonist Thank you

@@uncletom11000 Your are most welcome dear

Try reinstalling AutoDock Tools or check if the installation is complete; ensure you're following the tutorial steps correctly, as configuration files should generate automatically.

Try it with function key

VOSviewer ka istemal karke bibliometric analysis aur data visualization ke liye document banaya jaata hai.

We're removing ligands from crystallographic files to prepare the protein for docking with new ligands. While AlphaFold structures are useful, crystallographic data typically offers higher resolution and experimentally validated conformations, making it preferable for docking studies.

@@Axonist Makes sense but had a couple other questions: In theory, if the Alphafold predicted structure were to highly accurate (let's say it's at least as good as crystallographic data or better now or in the future) wouldn't removing the ligands alter the conformation of the protein in contrast to it's non-bonded state? How significant is this alteration? Also, would really appreciate it if you could point me in the right direction in order to learn a structured approach to using these tools through COLAB. Is this a viable route? Any disadvantages as opposed to just owning the necessary hardware? How do I master CHARMM? I've been banging my head against the wall for the better part of a year and would be really grateful for any guidance you could provide in this regard.

@@AlwaleedHadaidi Thanks for the questions! Ligand Removal Impact: Yes, removing ligands can alter a protein’s conformation since ligands often stabilize specific structures. Alphafold typically predicts unbound states, so this shift can be significant. Using COLAB: COLAB is a great starting point for learning these tools without expensive hardware, though it has computational limits. For larger projects, owning hardware might be better. Learning CHARMM: Start with official tutorials, documentation, and community forums. Persistence is key-every bit of progress counts! Feel free to reach out if you need more help!

@@AlwaleedHadaidi Great questions! Protein Conformation: Removing ligands can indeed alter the protein’s conformation, sometimes significantly, depending on the protein and ligand involved. This is why some studies start with the ligand-bound structure. Using Colab: Colab is a viable option for molecular docking, especially if you lack high-end hardware. It’s a great learning platform but has limitations like session timeouts and restricted memory. Learning CHARMM: Start with the official CHARMM tutorials and practice running simulations. Gradually, dive into research papers and forums to deepen your understanding. Stay persistent-it’s a challenging field, but you’ll improve with time. Good luck!

No, a 32-bit version of AutoDock Vina might not work properly on a 64-bit system. It's recommended to download the 64-bit version for compatibility.

Where can i download for 64 bit?

You can try downloading MGLTools from an alternative mirror site or use a different browser. If that doesn't work, consider checking the AutoDock Vina tutorial for additional guidance or solutions.