On Feb 14, 2011, at 7:24 PM, devicerandom wrote:
On 14/02/11 13:42, XAvier Periole wrote:
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
something
flexible.
I am afraid Martini is just not ready for simulating unfolded
proteins.
Any outcome of a simulation would have to be interpreted with CARE!
Agree with Xavier. I am working exactly on a coarse grained generic
FF that could allow this kind of simulations, but it's far from
being production ready -not an easy task at all. :)
thanks for your support "devicerandom"!
XAvier.
On Feb 14, 2011, at 2:09 PM, pol...@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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