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. 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.
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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