DS may have read some files incorrectly or there is something wrong with your input file. What is the format of your input file? Have you set your compounds as ligands in DS (try to do it manually)? I would check the ligands structure first. Is it correct? It seems there is something weird in the structure in this picture. Check for atoms without any bonds or maybe incorrect bonds that should not be there.

If that gray entity to the right of the error message is a depiction of your ligand, there is something seriously wrong with your ligand coordinates. The extra bonds suggest that your bond lengths are too short. Sometimes, this is seen if a 2D .sdf has been download instead of the energy-minimised 3D .sdf file.

Oh my god, that's exactly what it was. It was due to 2D structure of phytochemicals. You're spot on. Thank you so much, Ms. Honegger and Mr. Ragunathan.

Appreciate your input as well, Mr. Rabelo.

Ayesha Aslam I encountered the same problem. It said that the ligand is not a single fragment. I don't know what does it meant. Is that really due to 2D conformer?

I have downloaded 3d structures and still shows the error

@Annemarie Honegger, I'm faced with this same problem but I have tried searching for the 3D structure of my ligand(hydroxyl fullerene) but I haven't seen found it, so is there a way you can help me out. I was only able to get the 2D structure and have been told this same thing that Ligand is not a single fragment.

It is difficult to diagnose the problem without seeing the actual coordinate file(s). I would assume that generally this is a problem with the bond orders/hydrogens not being correctly defined. Therefore the number of bonds on some of the atoms are not correct for the atom type, the program finds open valences and therefore assumes the structure represents only a fragment of a larger structure. If you cannot find a proper experimental structure of your molecule, e.g. on https://ccdc.cam.ac.uk or a properly minimised 3D structural model, you need to model your molecule with a proper chemical modelling program.

Here are a few links:

Experimental structures:

Cambridge Structural Database: https://www.ccdc.cam.ac.uk

https://www.ccdc.cam.ac.uk/structures/?

Crystallography Open Database http://www.crystallography.net/cod/

Conversion from 2D formula to 3D

OpenBabel https://open-babel.readthedocs.io/en/latest/3DStructureGen/Overview.html

also see: https://www.researchgate.net/post/Can_anyone_provide_a_standalone_tool_for_2D_molecule_to_3D_molecule_conversion

answer by @Wandré Nunes de Pinho Veloso

for simple cases, also:

ChemDoodle https://web.chemdoodle.com/demos/2d-to-3d-coordinates

MolSoft https://www.molsoft.com/2dto3d.html

MolView https://molview.org

Thanks a lot, I'm searching these links now.

Hi Ayesha Aslam, I am having the same problem. How did you solve the problem? Or in other words, how can I obtain an energy minimized 3d ligand?

You can convert the 2D ligand to 3D by using Avogadro or OpenBarbel software. Hope this helps.

Dear Ayesha

It is due to your ligand preparation process. Check the pdbqt file of your ligand before docking. Maybe you will see a multi-fragment of the ligand. Something the wrong conversion has been made from 2D to 3D format. The solution is: back to the Openbabel conversion process and check all things out.

If you are encountering the error message "Ligand is not a single fragment" in BIOVIA Discovery Studio while trying to view the 2D diagram of certain phytochemicals, it indicates that the software is unable to properly fragment or divide the ligand molecule into distinct fragments. This issue seems to be specific to certain phytochemicals and not all of them. To resolve this problem, you may consider the following steps:

1. Check the ligand structure: Verify that the structure of the phytochemicals causing the error is correct and properly defined. Ensure that there are no missing atoms, bonds, or any other structural irregularities.

2. Modify ligand representation: Experiment with different representations of the ligand molecule. Try alternative file formats or representations, such as SMILES, MOL, or SDF, to see if the error persists. Sometimes, converting the ligand structure to a different format can resolve issues related to fragmentation.

3. Update Discovery Studio: Ensure that you are using the latest version of BIOVIA Discovery Studio. Check for any available software updates and install them if necessary. Updated versions often include bug fixes and improvements that can address such issues.

4. Contact technical support: If the problem persists, it is recommended to reach out to BIOVIA Discovery Studio's technical support team. Provide them with detailed information about the error message, the specific phytochemicals causing the problem, and any steps you have taken so far. They should be able to assist you further in resolving the issue.

Remember to save a backup of your work before attempting any modifications or updates to ensure the safety of your data.

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