[gmx-users] RMSD plots protein-protein complex

[Dr. Seema Mishra]

Moreover, this protein has ATP molecule also meaning it is a three molecule complex.



--------------------------------------------
On Tue, 22/1/19, Dr. Seema Mishra <seema_uoh at yahoo.com> wrote:

 Subject: Re: [gmx-users] RMSD plots protein-protein complex
 To: gmx-users at gromacs.org
 Date: Tuesday, 22 January, 2019, 1:47 AM
 
 I am also interested in answers to this
 thread. Can a protein only plot in a protein-peptide complex
 have increasing backbone RMSD values at 100 ns of
 simulations? If no, what needs to be done to stabilize
 trajectory?
 
 
 --------------------------------------------
 On Sun, 20/1/19, Justin Lemkul <jalemkul at vt.edu>
 wrote:
 
  Subject: Re: [gmx-users] RMSD plots
 protein-protein complex
  To: gmx-users at gromacs.org
  Date: Sunday, 20 January, 2019, 8:05
 PM
  
  
  
  On 1/18/19 11:55 AM, marzieh gharouni
 wrote:
  > Hello
  > I did a
  simulation of protein-protein
 interaction with Gromacs code.
  In
  > this simulation, the number of
 amino
  acids in each protein is about 230.
  > The
  simulation production run was 300ns.
 After analyzing
  trajectory, I
  > found that RMSD value of
  protein-protein complex fluctuated
 near 1.8 nm but
  > the single of each protein has
 RMSD plots
  around 0.35 nm. Other plots (rg ,
  > rmsf)
  of the protein-protein complex show my
 complex system is
  stable. But
  > I have a problem with the
  RMSD value (not behavior) of mix
 proteins. Is it
  > normal?
  > Please see
  share files
  > Rmsd of protein A-Protein B
  complex:
  > https://drive.google.com/file/d/16BoOdfUev2Bh7zgUCj4pOBAyPQLS_EJY/view?usp=sharing
  > Rmsd of Protein A:
  > https://drive.google.com/file/d/1QYt2rQQuNK4qqwp9O-k40uglSZaEYjAe/view?usp=sharing
  > Rmsd of protein B:
  > https://drive.google.com/file/d/1DYJ_jIUf-E9I8M38MrBxdh1tAtaIsBod/view?usp=sharing
  > Thanks in advance.
  
  The images mean nothing in the absence
 of your
  exact commands and 
  evidence of the groups
  you selected for analysis (copy and
 paste all 
  this directly from your terminal).
  
  -Justin
  
  -- 
 
 ==================================================
  
  Justin A. Lemkul, Ph.D.
  Assistant Professor
  Office: 301
  Fralin Hall
  Lab: 303 Engel Hall
  
  Virginia Tech Department of
  Biochemistry
  340 West Campus Dr.
  Blacksburg, VA 24061
  
  jalemkul at vt.edu
  | (540) 231-3129
  http://www.thelemkullab.com
  
 
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