Re: Alchemical FEP calculation involving glycine

From: Chris Chipot (
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
> ( 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.
> Thanks!
> - 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
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