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

[Kevin C Chan]

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
>
> ==================================================
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>