[gmx-users] Huge conformational change of ATP molecules
zruan1991 at gmail.com
Tue Feb 23 16:55:59 CET 2016
Thank you for the suggestions, but I don't think it is because of the PBC
artifacts. I do centered my protein and ligand with "-center -pbc mol"
option. The protein itself looks fine without any breaking. It's just the
ATP that moves out and stays at the outer surface of the protein. I don't
think it's possible in such a short time scale (20ns).
On Tue, Feb 23, 2016 at 4:32 AM, Mark Abraham <mark.j.abraham at gmail.com>
> It sounds like you are observing artefacts from
> On Tue, Feb 23, 2016 at 6:18 AM Zheng Ruan <zruan1991 at gmail.com> wrote:
> > Hi Gromacs Users,
> > I'm running 20ns MD simulation of a protein kinase with ATP bond. I use
> > amber99sb-ildn force field with parameters of ATP derived from the
> > of Richard Bryce.
> > What surprised me is that the ATP molecules displays a huge flexibility
> > conformational change. First, it slipped out from the starting binding
> > pocket. In addition, the plane of adenine ring and ribose sugar rotate to
> > about 180 degree after 10ns, making the ATP molecule looks weird. I never
> > run a MD of a protein with ligand before. Is this something normal? What
> > are possible causes for this? Maybe I should try some other ATP protein
> > complex to see if the same thing happens? Thank you!
> > Ruan
> > --
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