Hi,
The 'watershell' command uses a simple distance cutoffs: vdW radii are
not a part of the calculation.
Hope this helps,
-Dan
On Tue, Sep 8, 2015 at 9:08 AM, Travis Hughes <THughes.scripps.edu> wrote:
> In the watershell action command within cpptraj are distances from solute mask to solvent mask calculated based on centers of atoms or on VDW radius? For example would a water molecule be considered to be within 3.4 Angstroms of a solute atom where any part of the VDW radius of the TIP3P water lies within 3.4 Angstroms of the center of the solute atom?
>
> Thanks,
> Travis
>
> Travis Hughes, PhD
> Kojetin Lab
> Molecular Therapeutics
> The Scripps Research Institute
> Jupiter, FL
>
>
>
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--
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University of Utah
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Received on Tue Sep 08 2015 - 09:00:08 PDT
