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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