I am trying to dock a Calcium ion with my protein, however when I upload the pdb file for the ligand, I keep getting the error: Error in PDB file.
Issue when parsing the PDB file at line 1 .
ATOM/HETATM line does not meet the expected format
Below is my PDB file:
HETATM 1331 CA+2 CA2 A 364 19.958 32.985 27.661 1.00 30.94 Ca
END
I have browsed other topics related to the same issue, however I am unable to figure out why this error is appearing. Please help me out
Check carefully the column alignment - compare it with another pdb file. The format of the PDB files is very strict.
I have aligned it with respect to other PDB files and the alignment seems to be fine, however I get the error: DSSP failed to produce an output
Is there anything else I need to check?
Did you define it as a ligand when uploading the molecule?
Yes it was defined as ligand
Can you please share your input PDB files? Send them directly to us via email.
Note that ion docking is a not a scenario we have been actively supporting.
But we will check things.