[gmx-users] RMSD analysis

[Justin Lemkul]

On 6/6/17 4:01 PM, RAHUL SURESH wrote:
> 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?
> 

RMSD may be an indicator of something going on but by itself is useless.

Rg is only useful if the protein undergoes a large structural change or unfolding.

RMSF can be useful if the ensembles are converged; it is subject to big 
variation if you have any non-equilibrium sampling.

> 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?

Compare like with like.  I wouldn't believe comparisons between single 
trajectories of differing lengths have any meaning.

-Justin

> 
> 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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>> Gromacs Users mailing list
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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

==================================================