My result for the binding free energy of Zif268-Dna complex was - 206 kcal/mol
and delta G value was -111kcal/mol, from this values I calculated kd and the result was very far from the experimental values.
I made a pdb files from 1AAY.top and ( min.rst , heat.rst, density.rst, equil.rst, prod.rst) and viewed them in pymol to see where did I went wrong. I noticed that the zinc ion is moving away from its original position each step until finally it went out of the protein !!
Although I used the following restraint each step
Hold ZNA fixed
50.0
RES 108 110
END
END
How can I solve this problem?
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Received on Mon Mar 17 2014 - 08:00:03 PDT
