-
Notifications
You must be signed in to change notification settings - Fork 51
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
Mk_prepare_ligand fails for Vanadium-containing ligands #307
Comments
Hi @frgoe003 It takes two steps: (2) Even with the charging method, it's required to manually put in the additional atom types. In your local branch, please edit this file:
To declare a unique autodock atom type for generic V atoms. Now, you can run the command: My output is: We would like to know your feedback and suggestions in handling these ligands. Please let us know what you think and if you have any further questions. |
Hi @rwxayheee thank you for providing a solution to this, I have encountered what I believe to be the same issue with potassium and calcium metal complexes (not sure if these would cause complex bonds, I am new to this field): Output:
I will try out your branch, but I will look forward to completion of the PR, hope it goes forward. |
Thank you! I think the PR is ready; it's also up-to-date with the most recent I made this PR with the hope of encouraging more users/developers/chemists to help us explore this method, and tell us whether this is valid for their systems. This method is, at least, a working charge model with the gasteiger charge, which itself is not much more accurate in my opinion.. However, a very, very big limitation with this method is: It is completely blind to metal element types and more of a I do not see myself working on a new project that develops a new charge model of metal complexes for docking in the near future. However, I believe there are ways to physically derive the partial charges (for example, natural population analysis) and maybe modern, more recently developed charge models that are specialized for metal complexes. If you want to import charges from a third-party software, or a database, you can use the additional feature in this PR (#258 (comment)), which is currently available the I really hoped you could give it a try, but I understand the concerns you may have about using it. If you have a specific charge method that you would wish to be available in Meeko, please let us know and maybe we can work together to create a pythonic workflow to integrate it :D |
I noticed that the ligand preparation pipeline seems to fail for vanadium-containing ligands. Seems to be an issue with charge assignment:
Raised from meeko/writer.py
Code to reproduce:
mk_prepare_ligand.py -i AD9.sdf -o AD9.pdbqt
Examples:
AD9 from PDB 3MJX
-> AD9.sdf.zip
AOV from PDB 4AE3
The text was updated successfully, but these errors were encountered: