[gmx-users] Huge conformational change of ATP molecules

[Mark Abraham]

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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