[gmx-users] analyzing docking + MD results

[MD]

Excellent. Thank you Mark.
Happy holidays.
Ming

On Dec 23, 2017 10:14 PM, "Mark Abraham" <mark.j.abraham at gmail.com> wrote:

> Hi,
>
> Yes, GROMACS will do that. See
> http://www.alchemistry.org/wiki/Example_Free_Energy_Calculations (and many
> other resources)
>
> Mark
>
> On Sun, Dec 24, 2017 at 10:29 AM MD <refmac5 at gmail.com> wrote:
>
> > Hi Mark,
> >
> > Does GROMACS do that or I need to go with other software?
> >
> > Thank you,
> >
> > Ming
> >
> > On Dec 23, 2017 6:06 PM, "Mark Abraham" <mark.j.abraham at gmail.com>
> wrote:
> >
> > > Hi,
> > >
> > > Normally one would try to compute the relative free energy of binding
> > > between the two poses, but that is rather more costly than what you've
> > done
> > > so far.
> > >
> > > Mark
> > >
> > > On Sun, Dec 24, 2017, 07:24 MD <refmac5 at gmail.com> wrote:
> > >
> > > > Hi Gromacs folks,
> > > >
> > > > I want to look at protein peptide interaction. After docking two
> > > > conformations of the peptide emerged, and both of which make
> chemistry
> > > > sense and have similar low binding energies. (+-1 kj/mol). The
> distance
> > > > between the two conformations of the peptide is ~8A.
> > > >
> > > > Then I tried simulations on the two scenarios of protein peptide
> > > complexes
> > > > and the results showed the peptide only shifted very slightly in both
> > > > simulations. The rmsd, and energy dropping are all similar. I wonder
> if
> > > > there are other ways to make a judgement to tell which conformation
> of
> > > the
> > > > peptide makes more sense by analyzing their MD results?
> > > >
> > > > Thanks,
> > > >
> > > > Ming
> > > > --
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