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

[Justin Lemkul]

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

-- 
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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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