Atomic van-der-Waals (vdW) radii are calculated from atomic polarizabilities as recently introduced by Fedorov et al. (see their arXiv). In their work, they obtained a quantum-mechanical relation between atomic polarizabilities and vdW radii.
Rvdw(α)=θaα1/7,
where thetaa = 2.54 has been obtained by fitting to reference data for noble gases. Since the present model should be easily applicable to all elements up to Radon, an additional element-wise parameter thetab is introduced and fitted to reproduce theoretically determined vdW radii (see works of Rahm and Mantina).
Rvdw(α)=θaθbα1/7
We apply static atomic polarizabilities for the calculation of vdW radii. The graphic below depicts calculated vdW radii (vdwtype=rahm) for all atoms up to Radon (CN = 0, q = 0).
Define the Subcommand
> kallisto vdw options arguments
--chrg <int>
(optional, default: 0)
description:
absolute charge (qtotal) of the input structure (Lagrangian constraint)
--vdwtype <string>
(optional, default: rahm)
description:
reference atomic van der Waals radii
rahm: 10.1002/chem.201700610
truhlar: 10.1021/jp8111556
--angstrom (flag)
(optional, default: false)
description:
calculate van-der-Waals radii in Ångström
--out <string>
(optional)
description:
write output to file
input file is given as (positional) argument
Application
To calculate atomic van-der-Waals radii for a neutral charged Alanine-Glycine molecule, we call the subcommand vdw
> kallisto vdw alanine-glycine.xyz3.30656061715989223.381647596767163.43917501623035363.3118556928144883.37906803382489733.29676342031871043.47271511217215473.29763183191082473.30942150765038972.4209168925302162.41357300935865073.3564626256788082.54570858318946772.42740723203814172.52516142072901542.5270930292283392.4091413690502332.5401540257963372.5366469254835852.5536833297719026# Save output to file 'vdw'> kallisto vdw --out vdw alanine-glycine.xyz3.30656061715989223.381647596767163.43917501623035363.3118556928144883.37906803382489733.29676342031871043.47271511217215473.29763183191082473.30942150765038972.4209168925302162.41357300935865073.3564626256788082.54570858318946772.42740723203814172.52516142072901542.5270930292283392.4091413690502332.5401540257963372.5366469254835852.5536833297719026
Now we obtain a list of atomic van-der-Waals radii. However, we can furthermore calculate van-der-Waals radii for the cationic (or anionic) Alanine-Glycine molecule by incorporating the chrg option as described in the subcommand definition.