Dear Amber users:
I have a question about the QM/MM module in Amber9, I don't know if QM/MM can define the QM center dynamically, did not find it in manual. For example, for receptor+ligand simulation in Waterbox, first I define ligand and one water near to it as QM center, but later, after running MD for tens or hundreds ps, this water molecule may go far from the ligand and have no interaction with it, while another water come to the ligand, so, is it possible to change QM center dynamically during MD? Based on distance from ligand or some other criteria instead of using residue number?
Thank you very much for any help in advance :)
Yours sincerely,
aixiao
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Received on Fri May 26 2006 - 21:05:20 PDT
