[gmx-users] Simulation using Martini force field

[politr at fh.huji.ac.il]

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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