[gmx-users] Simulation using Martini force field

[XAvier Periole]

On Feb 14, 2011, at 11:43 PM, politr at fh.huji.ac.il wrote:

> Thank you very much for you reply. Can you please explain me why do  
> i need secondary structure file at all and why "secondary structure  
> is pre-defined and thus static throughout a simulation"? I didn't  
> see that something like this defined for lipids.
Have look at the Martini paper for protein (JCTC-2009) you might find  
some stuff quite instructive in there :))

FYI lipids do not have secondary structure or something that would  
succgest they could have different interacting behavior in function of  
their conformation.
> How do I use do_dssp to build the needed file? I saw that I need a  
> topology file in rder to use do_dssp. Where can I find this topology  
> file? I hope this is ok that I'm asking so many questions. Thank you  
> very much for your help.
No problem it just shows how it was a good idea to make a tutorial :))
have look there cgmartini.nl
> Regina
> Quoting "XAvier Periole" <x.periole at rug.nl>:
>
>>
>> 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!
>>
>> 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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