Dear Justin

What you said is true for bonded parameters, but how about the parameters of 
the nonbonded file?
Why Despite  any non-bonded parameters (Sigma, Epsilon) are considered between 
the gold atom and the other atoms , protein is stretched to the gold cluster  ?
What is the reason for this closing?Is not it true that when there is no 
epsilon and Sygma between two atoms, should not be move toward one another?

 
Fatemeh Ramezani
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