[gmx-users] analyzing docking + MD results

[Mark Abraham]

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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