AMBER: molecular dynamics simulation of protein containing Mg2+ cation

From: Ye Mei <>
Date: Fri, 1 Jul 2005 17:33:31 +0800

Dear Amber users

I am studying HIV-1 integrase, which contains a Mg2+ cation. Both D64 and D116 coordinate to this Mg2+ cation, together with water molecules and sometimes also with a ligand.
This coordination will strongly effect the charge distribution among Mg2+, D64, D116 and other coordinated molecules. I used the default FF03 parameters for all these residues, but it gave a very strong interaction between Mg2+ and a neutral ligand, like -150 Kcal/mol or even more. The ligand coordinate to Mg2+ with only 2 oxygen atoms, so -150 Kcal/mol, which mainly comes from coulomb interaction, is quite unreasonable. If we consider the charge redistribution among all these residues, the interaction should decrease.
But how can I treat them and get a reasonable result?
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 Fri Jul 01 2005 - 10:53:01 PDT
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