From: jostmey . (jostmey_at_gmail.com)
Date: Wed Mar 11 2015 - 17:57:02 CDT
Yeah, I see the extra CA atom for all the transformations involving
glycine. However, mutator seems to know to what to do with the extra
Would using CMAP corrections present any problems in the case of
glycine with its extra CA atom?
On Tue, Mar 10, 2015 at 5:59 AM, Chris Chipot <chipot_at_ks.uiuc.edu> wrote:
> 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
> Web: http://www.ks.uiuc.edu/~chipot
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-- Jared L. Ostmeyer University of Chicago (417) 540-8028
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