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Hi, amber users
I am doing a simulation for a enzyme-ligand binding complex. The ligand contains a triphosphoric acid group coordinating with Mg2+. So I use antechamber to generate the parameters for the ligand, and everything goes well. However, when I perform minimization and simulations, the end phosphoric acid group is deformed. In pymol, it seems that the three oxygen atoms bonded with each other. I do not know what is the problem, can anyone help me? By the way, I did not consider the Mg2+ into consideration when I make the parameters for the ligand, and I do not know if this is the problem.
Thank you so much!
Yan
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Received on Tue Aug 02 2016 - 17:30:02 PDT
