[gmx-users] Martini FF for Sec structure changes...

[XAvier Periole]

No, it does NOT!

HAve you red the paper?!

This implementation is an adoc representation to mimic specific  
sequences of short peptides! They do never for any secondary structure!

On Oct 10, 2012, at 3:05 PM, francesco oteri wrote:

> Hi rama,
> actually MARTINI has been further improved to allow secondary  
> structure
> change.
> The title is:
> *"Improving Internal Peptide Dynamics in the Coarse-Grained MARTINI  
> Model:
> Toward Large-Scale Simulations of Amyloid- and Elastin-like Peptides"*
>
> and here there is a link to the paper:
> http://dx.doi.org/10.1021/ct200876v
>
> Francesco
>
> 2012/10/10 XAvier Periole <x.periole at rug.nl>
>
>>
>> Nope, but on other softwares.
>>
>>
>> On Oct 10, 2012, at 2:50 PM, rama david wrote:
>>
>> Thank you for your reply,
>>>
>>> Are these Cg can be used in Gromacs.
>>>
>>> Thank you in advance.
>>>
>>> With best wishes and regards,
>>>
>>> Rama david
>>>
>>> On Wed, Oct 10, 2012 at 6:13 PM, XAvier Periole <x.periole at rug.nl>  
>>> wrote:
>>>
>>>
>>>> Martini FF cannot model changes in secondary structure ... other  
>>>> CG FF
>>>> can. You'll find them easily in the literature. Notably the ones  
>>>> from
>>>> Deserno or Derreumaux.
>>>>
>>>>
>>>> On Oct 10, 2012, at 2:03 PM, rama david wrote:
>>>>
>>>> Hi friends,
>>>>
>>>>>
>>>>> I planed to use the martini force-field for my simulation study of
>>>>> peptide.
>>>>>
>>>>> The peptides are initially alpha-helix in nature. As they come  
>>>>> together
>>>>> they formed amyloid fibre( Antiparallel Beta structure).
>>>>>
>>>>> Is it is possible to study the secondary structure backbone  
>>>>> study by
>>>>> martini force field.????
>>>>>
>>>>> I read in there tutorial that the Secondary structure is  
>>>>> predefined
>>>>> therefore they are statics through out the simulation.
>>>>> Conformational changes that  produces  changes in Sec structure  
>>>>> are out
>>>>> of
>>>>> scope in martini. only  tertiary structure are free defined to  
>>>>> change..
>>>>>
>>>>>
>>>>> So what to do ???
>>>>> How to use Martini FF to study secondary structure ???
>>>>>
>>>>> Is there any way to use coarse grained FF to use for study in Sec.
>>>>> structure???
>>>>>
>>>>>
>>>>> With Best wishes and regards,
>>>>> Rama David
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>
>
>
> -- 
> Cordiali saluti, Dr.Oteri Francesco
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