[AMBER] protein-ligand-metal complex simulation

From: Sangeetha B <sangeetha.bicpu.edu.in>
Date: Fri, 22 Jul 2011 15:48:40 +0530


I want to study the metal coordinated interaction of a protein-ligand
complex. The ligand interacts with my protein through two Mg2+ ions. I
have already done some simulations with protein-ligand complexes,
where I use antechamber to obtain the parameters for the ligand.
I have also referred the tutorial on
http://ambermd.org/tutorials/advanced/tutorial1_orig/ to generate .
But should we also define the co-ordinate bonds formed by the metal
with protein and ligand?
I do not have any idea of how to setup a simulation with metals. Can
anyone guide me with the steps involved in doing this simulation...
Any tutorials and references in this regard would be very helpful.

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Received on Fri Jul 22 2011 - 03:30:04 PDT
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