cannot recognize small molecule cofactor in protein receptor's PDB file

[hgg302]

my protein has a small molecule in the pdb file, when i try to dock the ligand, it always has this error:

Input residues {'A:311': 'AKG'} not in residue_templates

Trying to resolve unknown residues by building chemical templates...
******************** New Template Built ********************
{

causing my docking to fail.
is there anyway to fix this issue? like how to add my cofactor information into the residue_templates?

[rwxayheee]

Hi @hgg302

This is not an error. Or maybe you didn’t post the full message? What did you get? Usually the template building function is trying to auto process the cofactor for you, assuming that the structure (heavy atoms) is complete and the chemical identity matches with the registered residue in CCD (chemical component library).

And yesss you can register your own cofactors. We have a guide in our documentation to build a custom residue, see here: https://meeko.readthedocs.io/en/release-doc/py_build_temp.html#example-usage

I wrote this a while back. Let me know if this is still useful, or if you would want the functions to be present with a different example

[rwxayheee]

For docking with cofactors as part of receptor, we have this example for Vina:

https://meeko.readthedocs.io/en/release-doc/colab_examples.html#vina-basic-docking-with-cofactors