VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Feb 22 2010 - 15:41:08 CST

Irene,
  The new version of the code takes symmetry of the probe molecule
into account, thereby eliminating redundant orientations whereas the
old version did not. I've asked my colleague Jan Saam (who designed the
the new version of the algorithm) what the best parameters might be now.

Cheers,
  John

On Mon, Feb 22, 2010 at 09:19:56AM -1000, Irene Newhouse wrote:
> I notice that in the Cohen & al paper, 50 probe molecule orientations are
> used, yet the choices 1-6 are all for far fewer. I've also found another
> paper (not Shulten group) that used 400. Is there a consensus as to a
> reasonable number of probe molecule orientations to use?
>
> If I want to use 50, do I simply set orient 50 ?
>
> Thanks!
> Irene
>
> ----------------------------------------------------------------------
>
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-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
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Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
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