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

Peter C. Lai pcl at uab.edu
Sat May 26 01:34:44 CEST 2012

If there is tutorial for a system like yours it would probably have to be
(re)constructed from someone's publication. Multi-molecule systems shouldn't
be much different from your "typical" receptor-ligand system; if there isn't
a covalent bond between your dna and protein then life is even easier:
parameterize each as independent molecules, strip out everything after
the molecule topology, then use a system-wide .top that #includes 
each molecule's .itp file.

The integrator = steep scheme should not be sending whole molecules across 
the universe.

Does your anomaly happen even if you turn off periodic boundary 
conditions (pbc=no)?  (I noticed for my own system that sometimes doing a 
minimization in vacuum of a ligand by itself with pbc turned on causes the 
coordinates for an adjacent cell to be output, which when merged with the 
coordinates of the receptor causes the ligand to be located far away from
the receptor. I figured it's easier to just turn off pbc for vacuum
minimizations instead of trying to unwrap the pbc consistently.
Note that you can't use PME without PBC, you will need to use a pure
cutoff scheme (which will may generate a warning about artifacts but it's
EM so it's fine).

On 2012-05-25 04:01:52PM +0200, Matthias Ernst wrote:
> Hi,
> 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 
> this?
> 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 
> steps?
> Thank you for your help,
> Matthias
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Peter C. Lai			| University of Alabama-Birmingham
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