[gmx-users] Huge conformational change of ATP molecules

[Mark Abraham]

Hi,

Indeed that seems to short. So if one has excluded natural processes, the
artificial ones remain the only possible ones... Your process does have to
include a custom index group, for example... see
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions

Mark

On Tue, Feb 23, 2016 at 4:56 PM Zheng Ruan <zruan1991 at gmail.com> wrote:

> 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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