AMBER Archive (2005)

Subject: AMBER: simulation with Mg2+ ions and counter ions

From: Ye Mei (ymei_at_itcc.nju.edu.cn)
Date: Sat Jul 09 2005 - 01:54:16 CDT

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 an!
 ot!
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
ymei_at_itcc.nju.edu.cn
Institute of Theoretical and Computational Chemistry
Key Laboratory of Mesoscopic Chemistry
School of Chemistry and Chemical Engineering
Nanjing University
Nanjing 210093
P.R.China
2005-07-09

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