Assign Vdw Radii To A Protein Structure File (Pdb, Mol2, Etc)

Question

[Flow]

If I get a PDB or MOL2 formattted protein structure file, which method/software can I use to obtain the VDW radii for each of the protein atoms?

Answer 1

[Neilfws]

The physical properties of atoms are not encoded in protein structure file formats.

You'll need to locate that information elsewhere, but note that a "definitive" source is difficult to find. Some links:

• Wikipedia information
• periodictable.com
• Cambridge crystallographic data centre

[Flow]

yes, this "definitive" source is what I am trying to find, thanks

Answer 2

[Keith Callenberg]

One good method would be to use PDB2PQR. This tool is designed for preparing PDB structures for electrostatics calculations, however, this means replacing the B-factors column with the VDW radii.

Upload your PDB file to this webserver: http://kryptonite.nbcr.net/pdb2pqr/. You will have 6 options for "definitive" sources of radii:

• AMBER
• CHARMM
• PARSE
• PEOEPB
• SWANSON
• TYL06

They all have their own rationale. AMBER and CHARMM are safe bets for most applications, mostly because they are popular. I use PARSE in my work.

[Flow]

yes, this is the answer i was looking for!