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

[Smith, Micholas D.]

OPLS-AA 2001 (the one implimented in gromacs) can be a little slow in folding (in both my experience, and from   doi:10.1016/j.bpj.2009.04.061 ). That is not necessarily a bad thing if the peptide is suppose to take a while to fold. If you just want to get to the folded structure, and you don't care about the pathway, you could also use an enhanced sampling technique.

An alternative force-field that seems to handle beta structures pretty well, but can sometime accelerate the folding is the older GROMOS53A force-field; though since it is united atom, I have found that sometime the contacts don't quite match with NMR data.

Force-field choice is a non-trival, but largely difficult problem to deal with. In general, though, I tend to avoid the older Amber force-fields when simulating beta-rich peptides as have had a bias towards helical structures (see the references within the paper I noted above).

Good Luck,

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 SAPNA BORAH <sapnauser365 at gmail.com>
Sent: Wednesday, August 05, 2015 10:20 AM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Force-field bias???

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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