AMBER Archive (2009)

Subject: [AMBER] Any Comment, please

From: s. Bill (
Date: Tue Aug 11 2009 - 02:56:20 CDT


I am working on simulation of protein+ligand. According to the crystal
structural, the ligand bonds to Zinc active site of the protein by two
coordination bonds. I used QM/MM (PM3 Level) to simulate my system.
After minimization and heating (with constrain), the ligand lasted
bonded to the active site by two bonds. But, during equilibration, the
ligands started to change its position and formed ONLY one bond with the
zinc active site. I tried many models for the ligand and the active
site. but it didn't work.

I would appreciate any comment on what happened. Why the ligand didn't stay bonded with two bonds as in the crystal structure?

Thanks in advance;

S. Bill

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