[gmx-users] analyzing docking + MD results

Mark Abraham mark.j.abraham at gmail.com
Sun Dec 24 00:06:30 CET 2017


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 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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