[gmx-users] Simulation using Martini force field

[XAvier Periole]

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, 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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>
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