[gmx-users] Huge conformational change of ATP molecules

Zheng Ruan zruan1991 at gmail.com
Tue Feb 23 16:55:59 CET 2016


Hi Mark,

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).

Best,
Ruan

On Tue, Feb 23, 2016 at 4:32 AM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> It sounds like you are observing artefacts from
>
> http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
>
> Mark
>
> 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
> database
> > of Richard Bryce.
> >
> > What surprised me is that the ATP molecules displays a huge flexibility
> and
> > 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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