hi,
I have a PDB file of small molecules as chemical compounds (Figure 1) but I want to know their atom type like the PDB file of similar small molecules which has atom types such as CA, CB, ... in the third column(Figure 2). do we have any webserver or tools to know it?
I thank you for helping me with this problem.
best regards
Dear Ladan Mafakher
The arrangement of atoms in the second image is based on the structure of the PDB format, while a chemical molecule does not have a specific format, and that is why they are placed in order with the atoms by numbering, but with this, you can Change the names of the atoms manually in the text editing software manually.
best
Dear Milad
thanks for your answer. The problem I have is I do not know for example which carbon is Carbon alpha which is carbon Beta and...
I feel your recognition about alpha-carbon is wrong.
The HETATM lines show coordination of small molecules. Alpha-carbon (CA) and beta-carbon (CB) are positions of carbons in the protein structure. Therefore, no CA and CB lines are usually in the HETATM lines (except for the small ligand is a peptide).
thanks, Miki but when I used the HADDOCK webserver for docking small molecule-protein it needed to recognize the type of atom.
The nature of the atom is given in the last column of your PDB file. Protein and nucleic acids: appear in ATOM cards, and the precise type is defined there. Example:
ATOM 5 CB THR A 6 7.181 43.364 27.478 1.00 53.74 C
This is the C-Beta atom from residue 6 (a Threonine) in chain A.
There is no general rule for ligands/small molecules (all present as HETATM cards) except for those ligands (or ions, water...) that are so common in PDB files that there is a standard nomenclature for them. E.g. NAD, GOL etc.
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