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

[francesco oteri]

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