simulation of protein DNA complex

From: Dhiraj Srivastava (
Date: Mon Dec 27 2021 - 19:33:47 CST

Hi All
         I want to simulate the protein-DNA complex whose structure I
recently solved. However I want to simulate it with longer DNA than the one
in crystal structure to see how protein binding potentially affects the
conformation of nearby DNA sequence. The protein causes DNA bonding so I
can not generate an ideal DNA structure and simply replace the crystallized
DNA with the ideal one.
Is there any way I can extend the bend DNA in both directions before
starting the simulation?

Thank you

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