[gmx-users] Simulation using Martini force field
devicerandom at gmail.com
Mon Feb 14 19:24:20 CET 2011
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
> 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. :)
> 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.
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