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 - 11:00:03 PDT
