[gmx-developers] SASA / VDW radii

[Anton Feenstra]

David wrote:
> Values are:
> Atom	OLD (gromacs)	MSMS
> C     0.15		0.174
> F     0.12		0.14
> H     0.04		0.12
> N     0.110		0.154
> O     0.105		0.14
> S     0.16		0.18
> 
> Do you think it is a problem to replace the old values by the ones from
> MSMS?

Except for genbox, I see no problems. For genbox you should carefully check
what effects it will have on the generated solvent/solute interface. IIRC,
the solvent clipping is done based on a fraction of the sum of VdW radii
for solvent-solute atom pairs. This fraction should probably be re-tuned to
give the maximum amount of solvent possible witout bad contacts.

-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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