Відео

"Hi, please check the similarity between the two sequences. No synteny will be displayed if there is no significant similarity between them. You can use BLAST analysis to check for a significant match. If there isn't high similarity, you may consider core gene analysis or other comparison methods, such as Progressive Mauve Alignment, which may highlight evolutionarily conserved domains."

Are you trying to add gene labels into the figure?

Are you using molecules in PDBQT format? please check.

@@educont22 Yes I am Uning. I have uninstalled AutoDock and reinstalled it, but the problem persists. Whenever I try to open the PDBQT molecule in AutoDock, it just shows a blank screen. Could you please assist me in resolving this issue and ensuring that the PDBQT molecule can be successfully opened in AutoDock? Thanks Once again

@@drjagadishdasari2294 In that case, can you open your PDBQT file as a text file, and ensure that is not empty or contains some unexpected characters. Also, you can adjust the zoom level and check whether the zooming level is out of the visual field of your molecule. When you open the molecules, please also check that your molecule is selected in the left-hand panel (S L B C RMS L CI) at least one should be chosen.

No, it is still available. Check this link. mjsull.github.io/Easyfig/files.html

This part of the error message indicates that the software is encountering an issue related to the size of the search space volume specified for docking. AutoDock Vina has a limit on the size of the search space volume, and it seems that the specified volume exceeds this limit (which is set to 2700 Angstrom^3). You may need to adjust the size of your search space to be within this limit.

Do you want to create a profile plot in R or Python?

Let's try this, (1) sudo apt update, (2) deb cloud.r-project.org/bin/linux/ubuntu YOUR_UBUNTU_VERSION_HERE-cran40/ , (3) sudo apt update , (4) sudo apt install r-base, also check your typos and internet connectivity. Thank you.

In AutoDock Vina, the "Spacing" parameter in the configuration file (conf.txt) specifies the spacing (grid spacing) between grid points in the grid box used for docking. This parameter determines the resolution of the grid, which affects the accuracy and speed of the docking calculations. The default value used by AutoDock Vina is 1 Ångstrom. f the conf_vs.txt file generated by AutoDock Vina does not contain the Spacing parameter, you can add it manually to the configuration file (conf.txt). Typically, the Spacing parameter is set to a value between 0.375 Ångstrom and 1 Ångstrom. spacing = 1.0

The error message "Command line parse error: too many positional options" in AutoDock Vina typically indicates that there are too many arguments or options being passed to the command line. This error commonly occurs when the syntax of the command is incorrect, or when extra parameters are added that the program does not recognize. To resolve this issue, ensure that you are using the correct syntax for running AutoDock Vina from the command line. Here's an example of the basic syntax for running AutoDock Vina: vina --ligand <ligand.pdbqt> --receptor <receptor.pdbqt> --config <config.txt> --out <output.pdbqt>

Are you accessing the CMD using a non-administrator account?

Right-click on the MGLTools executable or shortcut. Select "Properties." Navigate to the "Compatibility" tab. Check the box for "Run this program in compatibility mode for:" and select a compatible operating system (e.g., Windows XP or Windows Vista). Click "Apply" and then "OK."

Were there any spelling mistakes in the script?

hi, i had the same error, i tried .\vina and it got solved!

There can be compatibility issues. You can simply open your PDB file in txt format check whether it follows standard PDB format required for Autodock Vina. Such as header formats. You can use other programs to correct PDB file, if there is any error in it.

run modeller as adminstrator. it'll work.

Ensure that the input parameters you are providing to AutoDock Vina are appropriate and do not result in division by zero. Double-check the values you are using for the grid dimensions, exhaustiveness, or any other relevant parameters.

@@educont22 The pdb file that my prof send to me had an error actually. Ty for the answer and also the video.

If you have a small number of files (for example in PDB format) you can convert them into smiles using various online software (Ex. cactus). If you have a large number of files to be converted into smiles, you can use other dedicated programs such as open babel. If use a particular database such as drugbank or Zinc, you can directly download structures in smiles format.

Have you tried running as administrator? please try and see.

If the model is less accurate, it can affect downstream analysis such as docking studies against intended ligands. Therefore quality of structure is important.

Thanks a lot!

Please ensure that the MGL Tools zip file you downloaded is complete and hasn't been corrupted during the download process. You can try re-downloading the file and attempting the extraction again.

Just seconds. It's very fast.

Thank you for your encouraging words.

Please check the new link. Sorry for the inconvenience.

It is possible but with a little complicated script by creating a batch script. I will try first and demonstrate how to do it. Thank you.

ua-cam.com/video/PPp7hobi-SA/v-deo.html

Thanks so much @@educont22 !

OSX Download the latest version of Easyfig (currently Easyfig_mac_2.1.tar.gz) and double click on the download to extract contents. Double-click on the Easyfig application to run Easyfig (known to work on Mac OS X versions 10.5 and 10.6). With later versions you may need to "Allow apps downloaded from anywhere", this option can be Preferences -> Security and Privacy (OSX Version 10.11).

@@educont22 my macOS version is 14.0 so EastFig 2.1 is too old to install