[gmx-users] analyzing docking + MD results
refmac5 at gmail.com
Sun Dec 24 00:28:57 CET 2017
Does GROMACS do that or I need to go with other software?
On Dec 23, 2017 6:06 PM, "Mark Abraham" <mark.j.abraham at gmail.com> wrote:
> 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.
> 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
> > 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
> > peptide makes more sense by analyzing their MD results?
> > Thanks,
> > Ming
> > --
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