[gmx-users] Protein stability using MARTINI

[Itamar Kass]

Thanks Mark for the replay,

I used VDW presentation to over come it.

Best,
Itamar


On 6/09/2010 6:33 PM, Mark Abraham wrote:
>
>
> ----- Original Message -----
> From: Itamar Kass <itamar.kass at monash.edu>
> Date: Monday, September 6, 2010 14:06
> Subject: [gmx-users] Protein stability using MARTINI
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>
> >  HI all,
> >
> > I am simulating a protein in water using the MARTINI (CG) force
> > field. My protein composed of few alpha-helices and a big tail
> > (~50AA) which is random coiled. I have built the simulation
> > system according to the procedure at
> > http://md.chem.rug.nl/cgmartini/index.php/tutorial/ubiquitin-in-
> > water .
> >
> > After a 10ns simulation, I have visualised the system using VMD.
> > It seems like the protein had dismantled to amino acids. I see
> > groups of bids moving freely in the system.
>
> I'm not sure what you mean here, but it seems likely that VMD's 
> heuristics for guessing where bonds between atoms might exist aren't 
> going to work well for a coarse-grained protein. There's probably a 
> standard solution, for which you should Google :-)
>
> Mark
>
> >
> > Any idea of the problem? Any idea how to fix it?
> >
> > PS I don't want to use elastic network for the random coil tail,
> > as I wish to capture as much conformation as possible.
> >
> > Thanks in advance,
> > Itamar.
> >
> > --
> >
> >
> > "In theory, there is no difference between theory and practice.
> > But, in practice, there is." - Jan L.A. van de Snepscheut
> >
> > ===========================================
> > | Itamar Kass, Ph.D.
> > | Postdoctoral Research Fellow
> > |
> > | Department of Biochemistry and Molecular Biology
> > | Building 77 Clayton Campus
> > | Wellington Road
> > | Monash University,
> > | Victoria 3800
> > | Australia
> > |
> > | Tel: +61 3 9902 9376
> > | Fax: +61 3 9902 9500
> > | E-mail: Itamar.Kass at monash.edu
> > ============================================
> >
> > --
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-- 


"In theory, there is no difference between theory and practice. But, in practice, there is." - Jan L.A. van de Snepscheut

===========================================
| Itamar Kass, Ph.D.
| Postdoctoral Research Fellow
|
| Department of Biochemistry and Molecular Biology
| Building 77 Clayton Campus
| Wellington Road
| Monash University,
| Victoria 3800
| Australia
|
| Tel: +61 3 9902 9376
| Fax: +61 3 9902 9500
| E-mail: Itamar.Kass at monash.edu
============================================

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