[gmx-users] Is it reasonable to get a bad Ramachandran plot after MD?
Kevin C Chan
cchan2242-c at my.cityu.edu.hk
Wed May 27 07:43:38 CEST 2015
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,
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
>> 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
>> care about the dihedral angles but still accurate enough to predict
> 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 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
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