Re: [AMBER] watershell cpptraj question

From: Daniel Roe <daniel.r.roe.gmail.com>
Date: Tue, 8 Sep 2015 09:54:01 -0600

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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> http://lists.ambermd.org/mailman/listinfo/amber



-- 
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Tue Sep 08 2015 - 09:00:08 PDT
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