[gmx-users] Simulation using Martini force field

[politr at fh.huji.ac.il]

regarding "parameterization of phosphorylated serine "
I checked the Martini papers and I couldn't find how it is done. Can  
somebody please instruct me.
In addition in JCTC paper from 2008 I saw that they simulated  
pentapeptides without imposing secondary structure. How can I do it?  
The problem is that there is no good tutorial how to use Martini  
(something general). If I still want to use Martini without imposing  
secondary structure how should I do it?
What tutorial is better to use the one for lipids or the one for  
proteins in water. I think I should explain what exactly I want to do.  
I want to simulate casein protein that is natively unstructured. The  
only thing that is known about this protein that it creates micelles.  
I just want to see if it possible to create micelles with Martini and  
I'm trying to understand what is the better way to run Martini taking  
into consideration the limitations of the force field and my system.  
As I'm not an expert in Gromacs neither in Martini force field I will  
appreciate very much any help for setting this simulation.
Thank you very much in advance.
Regina

n 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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