Dear AMBER users:
At the moment I am fighting with a problem, which I expected to be
trivial. I would like to use an ammonium ion (NH4+) in a simulation of a
protein-ligand complex. To make things easy, I just used antechamber for
the parameterization. The resulting charges look pretty reasonable.
However, when minimizing the system, the ammonium ion gets completely
deformed with all protons on one side of the nitrogen atom in an almost
perfect square. The binding site is very polar and I am wondering if
this could be causing the problem.
Is there any possible way to keep the tetrahedral conformation without
strongly constraining it?
Thank you very much.
Thomas
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon May 19 2014 - 06:00:03 PDT
