AMBER Archive (2006)

Subject: AMBER: QMMM simulation

From: amit_at_mbu.iisc.ernet.in
Date: Thu Jul 13 2006 - 13:38:48 CDT

Dear users,
I have used sander for qmmmm simulation. PM3 semi-empirical Hamiltonian
has been applied. In my sytems I have taken QM atoms as ATP. In the
simulation o-p bonds(p-o-p bonds are fine) of ATP is showing fluctuation
from 1.71 to 1.85Angs.
I have attached the md.in file for clarification. whether I am using any
wrong flags in the md.in script, which is leading to some weird results.

Thanks in advance

with regards,
amit

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