Re: Alchemical FEP calculation involving glycine

From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Thu Mar 12 2015 - 04:26:18 CDT

Technically the calculation will run fine, but with two copies of the
dihedral energy terms, ie the wrong backbone energetics! I am not totally
sure about the CMAP terms, if only the backbone atom types are taken into
account then they might be applied twice as well.

Jerome

On 11 March 2015 at 23:57, jostmey . <jostmey_at_gmail.com> wrote:

> 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
> atom.
>
> Would using CMAP corrections present any problems in the case of
> glycine with its extra CA atom?
>
> Thanks!
>
> - Jared
>
> On Tue, Mar 10, 2015 at 5:59 AM, Chris Chipot <chipot_at_ks.uiuc.edu> wrote:
> > Jared,
> >
> > the probable reason is that the library of hybrids only contains the
> > dual topologies for amino acids with a true side chain.
> >
> > Cheers,
> >
> > Chris
> >
> >
> >
> > 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.
> >>
> >> 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
> >
> > 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.
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> > _______________________________________________________________________
> >
>
>
>
> --
> Jared L. Ostmeyer
> University of Chicago
> (417) 540-8028
>
>

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