hello, I want to dock a small molecule with protein. but I got the error about the small molecule PDB file because the type of atom did not exist(smile.pdb) I did not get any error when I used another small molecule (4kn1-Q4J-aminopterin). I do not know how to find the atom type for my small molecule. also according to the HADDOCK library the pdb file of my compound(smile.pdb) is correct what is the problem and how can I solve it? CBP1 is my target protein
4kn1-Q4J-aminopterin.pdb (5.9 KB)
CBP1-Swiss-model-100.pdb (189.4 KB)
smiles.pdb (3.4 KB)
There is something wrong with your smiles.pdb file. It does not seem to follow proper PDB format
I am seeing something very strange, e.g. in Pymol
Hello, thanks for your answer.
could you please tell me what is the problem or send me a proper PDB file as an example to check my file with it or a webserver or tools to correct my PDB file? because the only difference that I found between smile.pdb fila and 4kn1-Q4J-aminopterin.pdb was the third column in which carbon, nitrogen type is mentioned as C1, C2 … in smile.pdb file but in 4kn1-Q4J-aminopterin.pdb file is Ca, Cb,…
Check carefully the columns - compare with a file from the PDB database.
Can you view your structure in for example pymol?