[gmx-users] Force-field bias???

[SAPNA BORAH]

Dear all,

Thank you for your answers which definitely clears some of my doubts. I am
trying to unfold a lectin tetramer protein that comprises largely of beta
strands, and I have used the OPLS ff, so far I have not been successful,
can OPLS be a problem at all??

Thanks..

Sapna Mayuri Borah
c/o Dr. A. N. Jha
Research student
Tezpur University,
India

On Wed, Aug 5, 2015 at 5:44 PM, Smith, Micholas D. <smithmd at ornl.gov> wrote:

> You should also note that force-field bias may be system dependent. So if
> you are unsure of the dynamics from the onset, you should likely test a
> variety of force-fields and/or try to find a comparison to NMR (or other)
> experimental methods.
>
> -Micholas
>
> ===================
> Micholas Dean Smith, PhD.
> Post-doctoral Research Associate
> University of Tennessee/Oak Ridge National Laboratory
> Center for Molecular Biophysics
>
> ________________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <
> gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Justin
> Lemkul <jalemkul at vt.edu>
> Sent: Wednesday, August 05, 2015 7:31 AM
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Force-field bias???
>
> On 8/5/15 6:24 AM, SAPNA BORAH wrote:
> > Dear all,
> >
> > I have a general query about unfolding simulations. Is there a bias among
> > force-fields selected for unfolding, i.e. is it possible that unfolding
> of
> > the protein may be different with a change in force fields applied?
> > Literature has given some support on this, however, I am not sure how
> this
> > may happen.
> >
>
> Yes, this is true.  It usually comes down to errors in the balance between
> intra-protein and protein-water interactions.  Incorrect balance favors
> either
> the folded or unfolded state.  No force field is perfect, but some are
> better
> than others and there's lots of literature on this topic regarding which
> are the
> most successful.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
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