Questions re: protein-DNA complex

From: Shirley Hui (
Date: Mon Jan 29 2007 - 16:20:02 CST


I an running an experiment to determine the interaction energy of a
zinc finger complexed with different DNA sequence fragments. I have
never done anything like this before or dealt with protein-DNA
complexes so I wanted some feedback on my method.

a) I started with the zinc finger/DNA complex as described by 1ZAA.pdb
b) I generated a different DNA sequence fragment (11 base pairs) of interest
c) I performed an RMSD alignment between the DNA from a) and the DNA from b)
d) I deleted the DNA a) from 1ZAA.pdb and replaced it with the aligned DNA b)
e) I solvated the complex in a water box
f) I neutralized the system
g) I ran a minimization until the gradient was around 10 (and did not
seem to change much)
h) I heated the system up to 300k
i) I equilibrated the system for 2000 timesteps (I found that after
2000 timesteps the energy values etc were not changing much)
j) I used NAMD energy to calculate the interaction energy between
protein and nucleic (vdw, elec, non bonded)

I had a few question being:

a) Does anyone have any comments on my method? I have never done this
before and wanted to know if this seemed correct? I obtained most of
the parameters for the simulation from NAMD tutorial (specifically the
Building Gramicidin A NAMD Tutorial) - however, maybe this is not

b) Should I actually "dock" the DNA from b) to the zinc finger rather
than performing a RMSD alignment and relying on the MD to yield a
favourable DNA-protein complex? What I have done seems naive.

c) Perhaps my simulation is not being run long enough (2000 time steps
seems a bit short I admit - but I see the energy values "plateauing"
after 2000 times steps which is why I did not run it for any longer).

Thank you for any help,

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