A good force field usually performs better (in terms of nuclear
dynamics) than poor ab initio calculations...
I am pretty sure that the AMBER force field will capture your hydrogen
bonds and I am almost sure it will be at least satisfactory for pi-pi
stacking interactions.
Dr. Vitaly V. Chaban, 430 Hutchison Hall
Dept. Chemistry, University of Rochester
120 Trustee Road, Rochester, NY 14627-0216
THE UNITED STATES OF AMERICA
On Mon, Jul 16, 2012 at 1:59 PM, jit mukherjee <jitiitkgp.gmail.com> wrote:
> Dear sir,
> I have some systems where pi-pi interaction and hydrogen bonding should
> take a vital role in determining the structure and energetics of the
> system. Now, I had a initial 'bad' structure of the system. So, I simulated
> it in amber classical force field. After simulation,I looked upon the
> structure and it seems that there is pi-pi stacking interaction(parallel in
> some systems and non-parallel) and also hydrogen bonding because the
> distance between the H-acceptor pair meets the criteria of hydrogen bonding.
>
> Now, I am trying to optimizing the simulated structure through the QM
> package TURBOMOLE with density functional theory but using a very low level
> method and basis set. After optimization, it seems that the pi-pi stacking
> interaction is no more in the structures!
>
> So,can I take the structure after simulation as the 'real' structure for
> the system or should I use high level quantum method to optimize the
> simulated structure. Actually, my systems are too big to avail the
> computational cost for the high level quantum method.
>
> Regards,
> jit
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Received on Mon Jul 16 2012 - 11:30:02 PDT
