[gmx-users] Simulation protocol for Protein-DNA-complex

Matthias Ernst Matthias.Ernst2 at student.kit.edu
Fri May 25 16:01:52 CEST 2012


I have a question regarding simulation of a protein-DNA-complex where 
the protein encloses the DNA double helix. I did not find a tutorial for 
a system of three rather big molecules like these, that's why I ask. If 
there is such, I would appreciate a hint.

I want to start with a crystal structure from PDB. When I do the steps 
in J. Lemkuls tutorial "Lysozyme in water", first thing would be an 
energy minimization in vacuo. Unfortunately, doing this I end up with 
the two strands of the DNA double helix being far away from the protein 
and seperated from each other. Can this result from clashes and 
therefore high energy in the system that allows the DNA strands to move 
"through" the protein or how else can this happen? And how can I prevent 

I mean, usually the protocol is:
- minimize system in vacuo
- add solvent and ions
- minimize again
- add thermostat and barostat
- simulate
Obviously, I cannot follow this if the first step already does not work. 
When I tried to skip in-vacuo-minimization and to minimize the system in 
solvent, it ended up bei either reaching machine precision without the 
maximum force being small enough or in the simulation, the atom were 
moving to fast. Would it be a good idea to use position restraints for 
the minimizations? If yes, for which part, in which order and in which 

Thank you for your help,

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