AMBER: simulation with Mg2+ ions and counter ions

From: Ye Mei <>
Date: Sat, 9 Jul 2005 14:54:16 +0800

Dear Amber users

Please help to check whether my simulation is reasonable.
I am trying to study a certain ligand binding to a protein with Mg2+ ions.. First, I docked this ligand to the binding site using autodock. In the docking procedure, I included neither the Mg2+ ion, counter ions nor the water molecules near the binding site. Then I took some binding modes and add Mg2+ to the protein and locate it where it was in the pdb file. 2 CL- ions were then added to this complex to neutralize the whole system. One of the CL- ion is binded to this Mg2+ ion with distance less than 3A. Periodic water box is added to this complex with 8 A between the protein and the unit boundary. Minimization and 2ns MD simulation under 300K were applied to this system. But I found that the CL- ion that is bonded to Mg2+ has not been pushed away by water molecules, but is still there. I guess maybe the simulation time is not long enough, though the whole system has seemed to in equilibrium for a very long time. But my computer resource is very limited, and I cannot give anot!
her ns simulation for each binding mode.
So, can I just stop here, and calculate the binding free energy? If not proper, is there any easy way for me to correct it?
Best regards,

Ye Mei
Institute of Theoretical and Computational Chemistry
Key Laboratory of Mesoscopic Chemistry
School of Chemistry and Chemical Engineering
Nanjing University
Nanjing 210093

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Received on Sat Jul 09 2005 - 08:53:00 PDT
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