[gmx-users] Simulation using Martini force field

XAvier Periole x.periole at rug.nl
Mon Feb 14 14:42:57 CET 2011

Dear Regina,

You have two problems:
1- the parameterization of phosphorylated serine should be done
following the same philosophy of Martini. Check the Martini papers
to see how this is done. In short partitioning is of primary importance.
2- you want to simulate unfolded protein ... indeed there is evidently
no persistent structure in such system and therefore the choice for
secondary structure would be coil in the Martini force field.
However the definition of "coil" for Martini has not been parameterize
to reproduce anything even close to what an unfolded protein, assuming
that we know what it looks like :)) The Martini "coil" is simply  

I am afraid Martini is just not ready for simulating unfolded proteins.
Any outcome of a simulation would have to be interpreted with CARE!


On Feb 14, 2011, at 2:09 PM, politr at fh.huji.ac.il wrote:

> Dear Gromacs users and developers,
> I'm interested to run simulation of natively unstructured protein  
> (casein), that can self assembly and create micelles, using Martini  
> force field. The initial structure of the monomer was created and  
> minimized using Sybyl. This protein includes also 4 phosporylated  
> serines. I'm trying to understand how should I set my system. I  
> started from the tutorial (http://md.chem.rug.nl/cgmartini/index.php/tutorial/ubiquitin-in-water 
> ) but I found that have no idea how to create a phosphorylated  
> serine inCG structure (I have it in my initial pdb). In addition, I  
> found that I need a secondary structure of the protein and I don't  
> have something like this. Moreover, this protein doesn't have one. I  
> will appreciated very much if somebody can help me and guide me a  
> little.
> Thank you very much in advance.
> Regina
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