Dear Chetna,
I am thankful to you for your help and support. I ploted
free energy profile as a function of two dihedral angles phi and Psi. I
also plotted free energy plot as function of PC1 (principal component 1)
and PC2 (principal component 2). In my free energy profile. there are two
minima. I do not know how to predict the structures of protein
corresponding to minima. Please let me know more details.
I highly appreciate your help.
Thanks
Mayank
On Wed, Apr 17, 2019 at 4:29 AM Chetna Tyagi <cheta231.gmail.com> wrote:
> Dear Mayank,
>
> you can reweight any distribution that you want. It can be for every
> dihedral angle distribution if you need or a phi-psi 2-dimensional
> distribution in case of producing free energy landscapes.
>
> In the example, they calculate phi-psi distribution for an alanine
> dipeptide which is ACE-ALA-NME so will have one phi angle distribution and
> other Psi angle distribution.
>
> As you protein is 398 residues long, you can probably only focus on
> functionally important residues and reweight their dihedral angle
> distribution. A better way would be to reweight your PC distribution to
> obtain free energy landscapes.
>
> I hope this helps.
>
> -Chetna
>
> On Wed, Apr 17, 2019 at 2:49 AM Mayank Dixit <mdixit.binghamton.edu>
> wrote:
>
> > Dear Users,
> > I have performed accelerated molecular dynamics
> > simulations (AMD) of protein in water by using dihedral boost and
> potential
> > boost.
> > I read the tutorial "
> > http://ambermd.org/tutorials/advanced/tutorial22/section3.htm". They are
> > saying to select two dihedral angles among backbone atoms of three
> > residues.
> > Please let me know which three residues of protein (number of residues
> > 398) I should select to reweight AMD results.
> > Please help me in fixing this issue.
> > Thanks and regards
> > MD
> > _______________________________________________
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> > AMBER.ambermd.org
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> >
>
>
> --
> Best wishes
> Chetna
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Received on Thu Apr 18 2019 - 08:00:01 PDT
