"charge", df.format(atom.getCharge()));
AtomElement.addAttribute(NonbondedForceElementChargeAttribute);
// Now look up the atomtype from the parm file
AtomType atomType = parameterStore.getAtomByType(atom.getType());
/*
* Convert values; getVdwRadius is in the form of r_min and in
* Angstroms, this needs to be converted to sigma and into nm.
*
* See section 14.6.1 of the theory OpenMM user's manual
*/
Double sigma = (atomType.getVdwRadius() * 2 * ANGSTROM_TO_NANOMETER)
/ (Math.pow(2.0, (1.0 / 6)));
df = new DecimalFormat("#.############");
Attribute NonbondedForceElementSigmaAttribute = new Attribute(
"sigma", df.format(sigma));
// Convert values; epsilon is in kcal/mol, but should be in kJ
Double epsilon = atomType.getVdwWellDepth() * KCAL_TO_KJOULES;
df = new DecimalFormat("#.#######");
Attribute NonbondedForceElementEpsilonAttribute = new Attribute(
"epsilon", df.format(epsilon));