From: Chris Chipot (chipot_at_ks.uiuc.edu)
Date: Tue Mar 10 2015 - 05:59:57 CDT
the probable reason is that the library of hybrids only contains the
dual topologies for amino acids with a true side chain.
On 3/9/15 11:58 PM, jostmey . wrote:
> Dr. Chipot,
> The page on the mutator plugin warns users about carrying out
> alchemical FEP calculations involving glycine
> (http://www.ks.uiuc.edu/Research/vmd/plugins/mutator/). Why does this
> warning exists? Is it because glycine tends to break protein secondary
> structure or is it because there will exists duplicate parameters that
> will throw off the calculation.
> - Jared
-- _______________________________________________________________________ Chris Chipot, Ph.D. Theoretical and Computational Biophysics Group 3047 Beckman Institute for Advanced Science and Technology University of Illinois at Urbana-Champaign 405 North Mathews Urbana, Illinois 61801 Phone: (217) 244-5493 E-mail: chipot_at_ks.uiuc.edu Christophe.Chipot_at_Univ-Lorraine.fr Web: http://www.ks.uiuc.edu/~chipot http://www.edam.uhp-nancy.fr It is hard for France to maintain a thirty-five-hour workweek when China and India have invented a thirty-five-hour workday. Thomas L. Friedman _______________________________________________________________________
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