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

[Tsjerk Wassenaar]

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: +41-(0)21-693-0322
> Institute of Chemical Sciences and Engineering ,        Fax: +41-(0)21-693-0320
> Laboratory of Computational Chemistry and Biochemistry  pascal.baillod at epfl.ch
> Room BCH 4121, Avenue Forel,                            http://lcbcpc21.epfl.ch
> CH-1015 Lausanne
> *******************************************************************************
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>



-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623