On 10/12/12 10:42 AM, rama david wrote:
Hi Gromacs friends,
I planed to use martini coarse grained ff to my simulation protocol.
My simulation protocol is:
I am placing two peptide at far distance.IAt these point i am using Gromos
FF they are initially in random coil structure.
Now when I run the simulation for 100 ns they are coming close in
antiparallel fashion.
Now I am placing more than two peptide ( 30) .I am using martini FF ,
I found that they are coming closer
I have practical result they are also showing random coil peptide changing
to the Beta sheet structure.
But my Query for Martini is :
As the martini ff is not representing the change in Secondary structure.
That the Secondary structure is predefined therefore they are statics
through out the simulation.
Is it wise to say by martini, peptide aggregate are beta sheet
structure..????
I don't think you can make that assertion with any confidence. I have limited
experience with MARTINI, but it is for this very reason - the secondary
structure limitations are significant. The force field is great for well-folded
proteins, but not for IDPs or amyloid systems.
Another Query:
Secondary structure are statics in simulation means that they are not
changing at all in simulation. Alpha helix is going to remain alpha helix.
or Secondary structure can be change but we are not able to determine in
which structure they will go.
No, the secondary structure is invariant. There are actual bonds in the
topology between backbone atoms that fix the structure.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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