[gmx-users] RMSD analysis

[RAHUL SURESH]

Dear Justin

I think I have confused so much.
Let me try to put it in simple way.

1.Can I compare Rmsd , rg , rmsf of protein-ligand complex with that of
monomer(just protein) to explain stability?

2. Time step of monomer(just protein) simulation is 150ns and
protein-ligand complex is 50ns. In this case is it valid to compare the
above analyses between monomer and complex?

Dear Justin I apologise if I am not to your mark to explain in better way.




On Wed, 7 Jun 2017 at 1:19 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 6/6/17 1:11 PM, RAHUL SURESH wrote:
> > 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?
>
> I'm not following.  You're talking about monomers and time intervals as if
> they're interchangeable.  What's the story?  Do you have a multimer?  Are
> you
> curious about demonstrating convergence?
>
> -Justin
>
> > 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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> --
> ==================================================
>
> 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*