[gmx-users] a residue move in extremely large scale in MD

Sat Aug 11 01:58:35 CEST 2012

Dear Dr. Dallas Warren, 

My protein is a protein-peptide complex. The residues I mentioned which moves in a large scope is from the peptide, it is the last 3rd residue of the peptide, a lysine. 
I compared this lysine position with the other residue positions (including the peptide binding pocket and the all the peptide residues) with PDB from different time intervals (total MD is 10 ns, and I extracted the PDB every 0.5 ns, and then I align all the PDB files and compared the relative position of this lysine in different PDB files), I find this lysine position changed most significantly during the whole 10 ns MD. 

In addition, will you please tell me how to analysis whether the phenomenon is from periodid boundary effect? I have no knowledge on how boundary effect affect the MD.  

Cheers, 

Acoot

________________________________
From: Dallas Warren <Dallas.Warren at monash.edu>
To: Discussion list for GROMACS users <gmx-users at gromacs.org> 
Sent: Thursday, 9 August 2012 8:40 AM
Subject: RE: [gmx-users] a residue move in extremely large scale in MD

No, I can't, since you are the one with all the information in front of you, and I only have a couple of sentences filtered through you on what is going on.

Some questions you can ask yourself to help answer the question you have:
    And what did the residue do while you watched the trajectory?
        Do you see it moving large distances?
        What about the residues directly adjacent to it?
    Where is it located within the protein?
    How did you measure that the residue moved a large distance with the PDB files?
        Just by looking at the coordinates?
        Or did you use a script?

In all likelihood what you are seeing here is simply a periodic boundary effect.  Which is why you should be actually watching the trajectory and what the residue itself does.  Seeing it with your eyes tells you what is going on much faster and it sinks in better too.

Catch ya,

Dr. Dallas Warren
Drug Discovery Biology
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at monash.edu
+61 3 9903 9304
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a nail. 

> -----Original Message-----
> From: gmx-users-bounces at gromacs.org [mailto:gmx-users-
> bounces at gromacs.org] On Behalf Of Acoot Brett
> Sent: Wednesday, 8 August 2012 4:55 PM
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] a residue move in extremely large scale in MD
> 
> Dear Catch ya,
> 
> I have watched the trajectory of the simulation. Besdies, I got the PDb
> file for the whole 10 ns MD every 500 ps. Then I compared all the PDB
> files generated, and it confirms that 1 specific residues moves in an
> extremely large space.
> 
> Can you give me an explaination on it?
> 
> Cheers,
> 
> Acoot
> 
> 
> ----- Original Message -----
> From: Dallas Warren <Dallas.Warren at monash.edu>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Cc:
> Sent: Wednesday, 8 August 2012 8:58 AM
> Subject: RE: [gmx-users] a residue move in extremely large scale in MD
> 
> What information has "told you" that you have large scale movement?
> Where did that information come from, how was it generated?  Have you
> watch the trajectory of this simulation to see how the residue actually
> moves?
> 
> Catch ya,
> 
> Dr. Dallas Warren
> Drug Discovery Biology
> Monash Institute of Pharmaceutical Sciences, Monash University
> 381 Royal Parade, Parkville VIC 3010
> dallas.warren at monash.edu
> +61 3 9903 9304
> ---------------------------------
> When the only tool you own is a hammer, every problem begins to
> resemble a nail.
> 
> > -----Original Message-----
> > From: gmx-users-bounces at gromacs.org [mailto:gmx-users-
> > bounces at gromacs.org] On Behalf Of Acoot Brett
> > Sent: Wednesday, 8 August 2012 8:30 AM
> > To: Discussion list for GROMACS users
> > Subject: Re: [gmx-users] a residue move in extremely large scale in
> MD
> >
> > Dear Marck,
> >
> > Will you please give me some suggestions on how to decide whether the
> > probelm is from periodic boundary conditions?
> >
> > Cheers,
> >
> > Acoot
> >
> >
> > ----- Original Message -----
> > From: Mark Abraham <Mark.Abraham at anu.edu.au>
> > To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> > Cc:
> > Sent: Monday, 6 August 2012 10:31 PM
> > Subject: Re: [gmx-users] a residue move in extremely large scale in
> MD
> >
> > On 6/08/2012 8:58 PM, Acoot Brett wrote:
> > >   Dear All,
> > >
> > > I have a protein with about 400 amino acids. I have done a
> production
> > MD of it. I find in the 400 amino acids, there is 1 amino acids,
> during
> > the whole MD process, this residue moves in a extremely large scope
> in
> > comparison with all the other residues.
> > > Do you think this single residue with extremely large-scale
> movement
> > in the whole MD has important biological function, or has no
> biological
> > function?
> >
> > I'd start by proving that it was not a problem with periodic boundary
> > conditions! If real, movement may or may not be indicative of
> > functional significance - the question is impossible to answer out of
> > context.
> >
> > Mark
> > -- gmx-users mailing list    gmx-users at gromacs.org
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