[gmx-users] Simulation using Martini force field
x.periole at rug.nl
Tue Feb 15 07:34:58 CET 2011
On Feb 14, 2011, at 7:24 PM, devicerandom wrote:
> On 14/02/11 13:42, XAvier Periole wrote:
>> 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
>> 2- you want to simulate unfolded protein ... indeed there is
>> 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
>> to reproduce anything even close to what an unfolded protein,
>> that we know what it looks like :)) The Martini "coil" is simply
>> I am afraid Martini is just not ready for simulating unfolded
>> Any outcome of a simulation would have to be interpreted with CARE!
> Agree with Xavier. I am working exactly on a coarse grained generic
> FF that could allow this kind of simulations, but it's far from
> being production ready -not an easy task at all. :)
thanks for your support "devicerandom"!
>> On Feb 14, 2011, at 2:09 PM, politr at 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
>>> ) 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
>>> very much if somebody can help me and guide me a little.
>>> Thank you very much in advance.
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