[gmx-users] Query

[Justin Lemkul]

On 5/19/15 6:29 AM, Priya Das wrote:
> Dear all,
>
> While generating RMSD plots of protein in presence of ligand, i am getting
> a RMSD of around 4.5 Angstrom around 10 ns after which the system is almost
> stable.
> Is it an acceptable RMSD?
> What is the acceptable range for RMSD for structures?
>

There is no general rule, and a number without context is meaningless.  How did 
you calculate the RMSD - backbone? heavy atoms? all atoms?  Does your protein 
have a lot of variable loops, and did you consider these?  Or did you just 
consider structured parts of the protein?  Did you include termini?  Did you 
watch the trajectory to see what's happening?

-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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