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

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?

pdb protein format structure structural
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updated by Keith Callenberg Keith Callenberg • written by Flow Flow

2 answers

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:

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written by Neilfws Neilfws

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

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written by Flow Flow

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.

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written by Keith Callenberg Keith Callenberg

yes, this is the answer i was looking for!

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written by Flow Flow

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