Re: [gmx-users] RMSF analysis

[Justin Lemkul]

On 10/9/13 4:09 PM, Sainitin Donakonda wrote:

What functional significance does it have, if any?  --- According to my
knowledge this reside is present in binding site.. and forms some hydrogen
bonds with ligand



Do you observe hydrogen bonds with the ligand?


What is the residue?  -- *Glutamic Acid*

What did you measure - RMSF of the whole residue, just the backbone, just
C-alpha, etc? --* I measured Just C-alpha atoms.*



So the backbone is fairly flexible.  Glutamic acid residues are very flexible, 
though the flexibility is usually due to side chain motions, hence why they are 
among the more difficult residues to assign in crystal structures.  Depending on 
the extent to which this residue is solvent exposed, this may explain your 
observations.  But again, this is a complete guess and other factors may be 
significant here, including sampling time, whether or not you are eliminating 
some time at the start of the simulation to allow for unrestrained equilibration 
(VERY significant for quantities like RMSF), and whether or not the observation 
is reproducible in multiple simulations.  The RMSF value you report is not 
especially large and may not mean anything at all, and its absolute value may 
not be convincing of any sort of argument.  Whether or not it changes depending 
on conditions like presence or absence of a ligand may be more interesting, but 
as hopefully these last few sentences show, there is very little point in anyone 
guessing at functional implications from one vaguely described outcome ;)


-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
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Re: [gmx-users] RMSF analysis

[Gianluca Interlandi]

Is that residue in a loop?

Gianluca

On Wed, 9 Oct 2013, Sainitin Donakonda wrote:


Hi all,

I recently performed MD simulation of protein - ligand complex..and
analyzed its trajectory using RMSF tool in gromacs.

This analysis revealed particular residue in binding site of protein showed
quite high fluctuation around 0.30 nm but other residues were in range of
0.15 to 0.20

Can any body explain why this particular residue have  high RMSF value in
compared to other residues

Thanks,
Nitin
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-
Gianluca Interlandi, PhD gianl...@u.washington.edu
+1 (206) 685 4435
http://artemide.bioeng.washington.edu/

Research Scientist at the Department of Bioengineering
at the University of Washington, Seattle WA U.S.A.
-
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Re: [gmx-users] RMSF analysis

[Sainitin Donakonda]

What functional significance does it have, if any?  --- According to my
knowledge this reside is present in binding site.. and forms some hydrogen
bonds with ligand

What is the residue?  -- *Glutamic Acid*

What did you measure - RMSF of the whole residue, just the backbone, just
C-alpha, etc? --* I measured Just C-alpha atoms.*

Let me know


On Wed, Oct 9, 2013 at 9:47 PM, Justin Lemkul  wrote:

>
>
> On 10/9/13 3:29 PM, Sainitin Donakonda wrote:
>
>> Hi all,
>>
>> I recently performed MD simulation of protein - ligand complex..and
>> analyzed its trajectory using RMSF tool in gromacs.
>>
>> This analysis revealed particular residue in binding site of protein
>> showed
>> quite high fluctuation around 0.30 nm but other residues were in range of
>> 0.15 to 0.20
>>
>> Can any body explain why this particular residue have  high RMSF value in
>> compared to other residues
>>
>>
> Doubtful, at least not without considerably more information.  What
> functional significance does it have, if any?  What is the residue?  What
> did you measure - RMSF of the whole residue, just the backbone, just
> C-alpha, etc?
>
> Higher RMSF means the residue flops around more, i.e. your outcome
> indicates that the residue deviates from the average position to a greater
> extent than the other residues.  Whether or not this actually means
> anything at all depends on your knowledge of the nature of the
> protein-ligand complex and the answers to the questions posed above.
>
> -Justin
>
> --
> ==**
>
> Justin A. Lemkul, Ph.D.
> Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul@outerbanks.umaryland.**edu  | 
> (410)
> 706-7441
>
> ==**
> --
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Re: [gmx-users] RMSF analysis

[Justin Lemkul]

On 10/9/13 3:29 PM, Sainitin Donakonda wrote:

Hi all,

I recently performed MD simulation of protein - ligand complex..and
analyzed its trajectory using RMSF tool in gromacs.

This analysis revealed particular residue in binding site of protein showed
quite high fluctuation around 0.30 nm but other residues were in range of
0.15 to 0.20

Can any body explain why this particular residue have  high RMSF value in
compared to other residues



Doubtful, at least not without considerably more information.  What functional 
significance does it have, if any?  What is the residue?  What did you measure - 
RMSF of the whole residue, just the backbone, just C-alpha, etc?


Higher RMSF means the residue flops around more, i.e. your outcome indicates 
that the residue deviates from the average position to a greater extent than the 
other residues.  Whether or not this actually means anything at all depends on 
your knowledge of the nature of the protein-ligand complex and the answers to 
the questions posed above.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
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Re: [gmx-users] rmsf analysis

[Ankita naithani]

Hi,

It should be able to find md.tpr unless your file is named something
else or you are issuing the command from other directory.

On Wed, Mar 13, 2013 at 9:31 AM, vansh  wrote:
> to analyse the flexibility of the protein i used tge command
> g_rmsf -s md.tpr -f traj.xtc -oq
>
> but its showing that - can not open md.tpr file
>
> as i am new to it cant figure it outany suggestions...
>
>
>
> -
> thanks in advance :)
> --
> View this message in context: 
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-- 
Ankita Naithani
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