[gmx-users] Is it reasonable to get a bad Ramachandran plot after MD?

[Tsjerk Wassenaar]

Hi Kevin,

What happens if you bring the temperature down gradually to experimental
(crystallization) conditions?

For each residue, what is the proportion of time spent in 'forbidden'
regions? Is there a correlation with B-factor? And what would be the effect
of the outliers on the experimental observable (the scattering pattern, not
the fitted, energy minimized structure)?

Cheers,

Tsjerk

On Wed, May 27, 2015 at 7:43 AM, Kevin C Chan <cchan2242-c at my.cityu.edu.hk>
wrote:

> Dear Justin,
>
> Thanks for the reply. I was using CHARMM27 force-field. In fact, it was a
> MDFF simulations in NAMD raising my interest as the resulted structure had
> 5% outliers and was doubted by experimentalists. I also checked other
> conventional MD results and the % of outliers vary among structures from
> <1% to 5% (all using the same CHARMM force-field).
>
> I do not know specifically which residues lie in those regions, can anyone
> suggest a more comprehensive analysis tool for Ramachandran plot?
>
> Thanks in advance,
> Kevin
>
> On Fri, May 15, 2015 at 12:41 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
> >
> >
> > On 5/14/15 8:51 AM, Kevin C Chan wrote:
> >
> >> Dear Users,
> >>
> >> As the title states, I am wondering the validity behind the outliers
> >> appear
> >> in a Ramachandran plot of structure after MD. I only have little data on
> >> this, but for a 10,000-atom protein, portion of outlier can increase
> from
> >> 0.7% to 5.0%. Is this explainable? Or it simply means my force-field
> does
> >> not
> >> care about the dihedral angles but still accurate enough to predict
> >> protein
> >> dynamics?
> >>
> >>
> > Which residues lie in those regions?  What force field are you using?  Is
> > that force field known to produce only-allowable Ramachandran regions.
> > Note that glycine can do just about anything it likes...
> >
> > -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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-- 
Tsjerk A. Wassenaar, Ph.D.