[gmx-users] Simulation using Martini force field

[devicerandom]

On 15/02/11 06:34, XAvier Periole wrote:
>>> 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"!

Uh... was it sarcastic or are you serious? (in any case: welcome!)


>>> 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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