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, pol...@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.peri...@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, pol...@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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