[gmx-users] Re: Dose the GROMOS FF favour beta-sheets?

[pascal.baillod at epfl.ch]

Hi Tsjerk,

Thank you very much for your answer! I use the 43a1 force field. Here are two
references of comparative force field studies that suggest that gromos-g96
favours beta sheets. I would be interested in any other study with similar or
different conclusions.

Yoda, T.; Sugita, Y. & Okamoto, Y. Secondary-structure preference of
force-fields for proteins evaluated by generalized-ensemble simulations Chemical
Physics, 2004, 307, 269-283

Yuguang, M.; Kosov, D. S. & Stock, G. Conformational Dynamics of Trialanine in
Water. 2. Comparison of AMBER, CHARMM, GROMOS, and OPLS Force Fields to NMR and
Infrared Experiments J Phys Chem B, 2003, 107, 5064-5073

Best regards,

Pascal


> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Wed, 20 Feb 2008 20:12:59 +0100
> From: "Tsjerk Wassenaar" <tsjerkw at gmail.com>
> Subject: Re: [gmx-users] Dose the GROMOS FF favour beta-sheets?
> To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
> Message-ID:
> 	<8ff898150802201112h4fa987a7j7c646b38ce824147 at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
> 
> Hi Pascal,
> 
> Please specify the (Gromos) force field used further. There seems to
> be something with the 53a5/6 series in terms of alpha helix / beta
> sheet preference. I'm not sure whether this has been fixed already. I
> don't recall having heard of such an issue with the 43a2/45a3 series.
> But these have there own problems of course, just as any force field
> has. Keep up the development!
> 
> Anyway, hope this is useful to you.
> 
> Cheers,
> 
> Tsjerk
> 
> On Feb 20, 2008 5:41 PM,  <pascal.baillod at epfl.ch> wrote:
> >
> > Hi everybody,
> >
> > I am doing some protein unfolding simulations and getting some new,
> compact and
> > beta-sheet rich unfolded states.I have read 2-3 papers comparing force
> fields
> > and suggesting that the gromos force field might overstabilize
> beta-sheets. Has
> > anybody else obtained beta -rich unfolded conformations in protein
> unfolding
> > simulations, or know of any other relevant reference I might have
> overseen?
> >
> > Thanks a lot in advance!!
> >
> > Pascal
> >
> >
> >
> *******************************************************************************
> > Pascal Baillod (PhD student)
> >
> *******************************************************************************
> > Swiss Federal Institute of Technology EPFL              Tel:
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> 
> 
> -- 
> Tsjerk A. Wassenaar, Ph.D.
> Junior UD (post-doc)
> Biomolecular NMR, Bijvoet Center
> Utrecht University
> Padualaan 8
> 3584 CH Utrecht
> The Netherlands
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>