steered molecular dynamics docking

From: WONG Hua (
Date: Wed May 18 2005 - 04:55:37 CDT


I want to do steered molecular dynamics and docking on NAMD, and I would like some piece of advice.

I am working on a DNA-protein complex that I had first docked with the software HEX ( in order to have a good orientation of the ligand on the receptor DNA ).
I then separated both macromolecule again (the center of mass of each molecule is separated with 30A).

My goal is to apply a force on the ligand and do some sort of docking using MD.

What I have difficulty to set, is :
force constant and velocity

What would be sensible values to avoid having the ligand going too fast and tearing my DNA strand apart ?

here are the current SMD parameter I determined using an unsolvated system
# vecteur prot-->dna [ -4.198, 29.533, 1.045]
SMD on
SMDFile output_neutralization/SMDconformation.pdb
SMDk 0.5
SMDVel 0.0005
SMDDir 4.198 -29.533 -1.045
SMDOutputFreq 20

The actual system is a DNA-protein complex in a water sphere.


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