[gmx-users] Simulation using Martini force field

[politr at fh.huji.ac.il]

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. 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.
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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