[gmx-users] Simulation using Martini force field

Ran Friedman ran.friedman at lnu.se
Tue Feb 15 07:40:34 CET 2011

Hi Regina,

Most CG force fields for proteins are less versatile than all-atom force fields and are simply not adequate for every application. As the secondary structure is determined a priori, you cannot model secondary structure changes, as probably happen during aggregation - even if the definition of the unordered protein was correct. You probably need to choose another FF or method. The UNRES FF from the Scheraga group doesn't suffer from this limitation, but isn't implemented in Gromacs and may have other caveats.

You can take a look at the MARTINI web page and paper (on the protein FF) about the definition of secondary structure.

Best regards,
Ran Friedman
Biträdande Lektor (Assistant Professor)

Linnaeus University
School of Natural Sciences
391 82 Kalmar, Sweden

Norrgård, room 328d
+46 480 446 290 Telephone
+46 76 207 8763 Mobile
ran.friedman at lnu.se

Message: 1
Date: Tue, 15 Feb 2011 00:43:51 +0200
From: politr at fh.huji.ac.il
Subject: Re: [gmx-users] Simulation using Martini force field
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Message-ID: <20110215004351.13575htmiyeizi0w at webmail.huji.ac.il>
Content-Type: text/plain;       charset=UTF-8;  DelSp="Yes";    format="flowed"

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.
Quoting "XAvier Periole" <x.periole at 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, 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
>> (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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