[gmx-users] RMSD analysis

[RAHUL SURESH]

Dear Justin

Thank you. I am considering  Rmsd rmsf rg as just supplementary analysis
for my study.  My aim to analyse  conformational change in protein. I would
like to bring a note on protein stability after ligand binding. I don't
know to which part of monomer I can compare the rmsd of complex with.
First 50ns or last .. can you please help me with this?
On Tue, 6 Jun 2017 at 5:35 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 6/6/17 2:12 AM, RAHUL SURESH wrote:
> > Dear Users
> >
> > *Exp procedure:*
> > I have simulated the protein monomer for 150ns. Using the 150ns
> conformer,
> > ligand is docked to the protein using autodock and the simulation is
> > carried out for 50ns.
> >
> > *Analysis:*
> >
> > Is it possible to compare my RMSD, RMSF, ROG analysis of complex system
> > with that of monomer? If yes which part of the monomer trajectory should
> be
> > considered.?
> >
>
> This is up to you to determine in light of whatever your goals are in
> running
> the simulation.  What are you trying to test or determine?  Unless the
> protein's
> stability is seriously impacted by the ligand, RMSD and Rg are useless.
> RMSF
> might be useful if there are motions that are amplified or damped by ligand
> binding.  Run the analysis and see what happens on a per-residue basis.
>
> -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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-- 
*Regards,*
*Rahul Suresh*
*Research Scholar*
*Bharathiar University*
*Coimbatore*