RosettaCommons
RFD3 fail to recognize ligand name, and replace the three letter ligand name into ALA after inference
Hi the creators of RFD3!
I named my ligand as LIG in input.pdb, but it reported as: ValueError: Transforms failed at stage CreateDesignReferenceFeatures: could not broadcast input array from shape (15,3) into shape (28,3).
I am quite sure that the molecule structure with 28 heavy atoms is correct.
Then I tried VD3 as the name, similar error occured though.
So I finally used UNK as name. The inference normally finished, however, the name was replaced as ALA in the predicted output cif file.
How to fix this, I am worried that the inccorect recognition could form inccorect ligand conformation.
Looking forward your feedback, Thanks!
I have the same issue. My “LIG” was generated from an AF3 prediction. The input array was expected to have the shape(48, 3), but it came out as (15, 3). After renaming the ligand from “LIG” to “A86”, the number of missing atoms decreased, and the input array changed to (46, 3).
18:05:21 WARNING atomworks.ml.transforms.rdkit_utils: Initial conformer generation based on distance geometry failed. Successful: 0. Falling back to generating a conformer starting from random coordinates. 18:05:23 WARNING atomworks.ml.transforms.rdkit_utils: Failed to generate 2 conformers for ccd_code='A86'. Falling back to idealized conformer from the CCD. Error message: Function <function generate_conformers at 0x7f67d16aa160> timed out after 2.0 seconds 18:05:31 WARNING atomworks.ml: Atom O6 not found in conformer for residue A86 with atom_names=array(['C1', 'O1', 'C2', 'O2', 'C3', 'O3', 'C4', 'O4', 'C5', 'O5', 'C6', 'O6', 'C7', 'C8', 'C9', 'C10', 'C11', 'C12', 'C13', 'C14', 'C15', 'C16', 'C17', 'C18', 'C19', 'C20', 'C21', 'C22', 'C23', 'C24', 'C25', 'C26', 'C27', 'C28', 'C29', 'C30', 'C31', 'C32', 'C33', 'C34', 'C35', 'C36', 'C37', 'C38', 'C39', 'C40', 'C41', 'C42'], dtype='<U6'). 18:05:31 WARNING atomworks.ml: Atom C42 not found in conformer for residue A86 with atom_names=array(['C1', 'O1', 'C2', 'O2', 'C3', 'O3', 'C4', 'O4', 'C5', 'O5', 'C6', 'O6', 'C7', 'C8', 'C9', 'C10', 'C11', 'C12', 'C13', 'C14', 'C15', 'C16', 'C17', 'C18', 'C19', 'C20', 'C21', 'C22', 'C23', 'C24', 'C25', 'C26', 'C27', 'C28', 'C29', 'C30', 'C31', 'C32', 'C33', 'C34', 'C35', 'C36', 'C37', 'C38', 'C39', 'C40', 'C41', 'C42'], dtype='<U6'). ... ValueError: Transforms failed at stage
CreateDesignReferenceFeatures: could not broadcast input array from shape (46,3) into shape (48,3)
Hi! This error usually happens if there's a name conflict with your ligand name and a ligand that's in the ccd; it's trying to use the CCD reference conformer for LIG which is not the same shape as yours. You can name your ligand something like L:G (with a semicolon) which will make sure it's non-ccd
