From: Axel Kohlmeyer (
Date: Sat Dec 13 2008 - 16:37:11 CST

On Sat, 13 Dec 2008, Lan Hua wrote:

LH> Hi,
LH> I have a simple question about the definition of the keyword "radius" of
LH> the atom selection.

LH> I thought the value I obtained using $sel get {radius} was van der Waals
LH> radius, but it seems not consistent with what I calculated by r0/2^(1/6)
LH> where r0 is from parm99.dat. So does the keyword "radius" mean van der Waals
LH> radius? Thank you in advance.

please note that van der waals radii are not the sigma
values from lennard-jones interactions.

radius values are - when supported - taken from the provided
coordinate file (e.g. for PQR format files) or a from table
with the following properties.

 * corresponding table of VDW radii.
 * van der Waals radii are taken from A. Bondi,
 * J. Phys. Chem., 68, 441 - 452, 1964,
 * except the value for H, which is taken from R.S. Rowland & R. Taylor,
 * J.Phys.Chem., 100, 7384 - 7391, 1996. Radii that are not available in
 * either of these publications have RvdW = 2.00 <C5>.
 * The radii for Ions (Na, K, Cl, Ca, Mg, and Cs are based on the CHARMM27
 * Rmin/2 parameters for (SOD, POT, CLA, CAL, MG, CES) by default.


LH> Best,
LH> Lan

Axel Kohlmeyer
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
If you make something idiot-proof, the universe creates a better idiot.