cannot generate topology

[syhpd]

hello, may god bless you

could you help me to find the mistake between this two (ligand example and my ligand)

ligand example that you gave

my ligand

i have the same issues as evryone before me

i have given a try to what you suggest to recheck the ligand and still, it cannot work for me. is there a chance that the syntax cannot read a more complex ligand structure?

Best, Dio

[pablo-arantes]

Hi @syhpd,

Thank you for letting me know about the issue. Can you please send me an example of your pdb files? Just looking the image file like you sent, is difficult to figure out what is wrong. I want to try by myself and see If I need to change something in the code.

Thank you.

Best,

Pablo

[syhpd]

thanks for your feedback

Work.zip

hope it will work soon,

Dio

[pablo-arantes]

Hi @syhpd,

Thanks for the files. I have several points regarding your issue: 1) Your ligand is not a small molecule or small drug, it's a complex structure with carbohydrates and aromatic rings.
2) Our notebook uses RDkit to add the hydrogens in the small molecules. It works well for aliphatic chains or aromatic rings, but when you submit a more complex molecule, like yours, we can have issue in the protonation step. It's common, the protonation of your molecule is an important step in the preparation of the system. 3) I tried your molecule, and we do have an issue with the protonation of the carbohydrates rings. My suggestions are to submit the molecule already with the hydrogens in the right protonation state and then select no on Add_ligand_hydrogens option in the first cell (follow the image below). 4) I tried to add the hydrogens in Pymol and then submit the molecule in the notebook, and it worked well, the topology was created in the right way. One significant observation, your molecule is not small, so for the topology generation cell it took me around 12 minutes to create the topology. You can find the PDB file of your molecule with the right protonation state attached here. 5) Next time, if you have a complex molecule like that, it's better to upload already with the right protonation state. ;-) BTW, I will put a disclaimer in the notebook regarding the protonation of more complex molecules.

Follow some pictures of your system working in the notebook:

I hope it helps. Please, let me know if you have any question.

Thank you.

Pablo DCS_2.zip

[syhpd]

thanks for the helping and pointing the issues.

it works now, , next time i will do wht u suggested

Thankyou in advance.

Dio