[gmx-users] RMSD plots protein-peptide complex

[Dr. Seema Mishra]

Ok I understand. We create index groups for backbone atoms of selected protein only. I made index group for whole residues of selected protein. Will do again.  Ok then let us see.


--------------------------------------------
On Fri, 11/1/19, Justin Lemkul <jalemkul at vt.edu> wrote:

 Subject: Re: [gmx-users] RMSD plots protein-peptide complex
 To: gmx-users at gromacs.org
 Date: Friday, 11 January, 2019, 1:56 AM
 
 
 
 On 1/10/19 8:23 PM, Dr. Seema Mishra wrote:
 > Ok so I created index group already and
 fed it ti trjconv and g_rms. But while selecting atoms in
 g_rms stage if we select 22 (for index group) then all atoms
 of index group will be selected. We want inly backbone atoms
 of index group. I thought my commands just written before
 here would work. Otherwise, How to get that?
 
 Like I said before, you need
 to create an index group that has the atoms 
 you want to analyze. I don't know what
 group 22 is and you're not 
 posting
 complete information. If you want the backbone of the
 protein 
 (receptor), then create an index
 group with just those atoms so you can 
 use
 it for analysis.
 
 -Justin
 
 >
 --------------------------------------------
 > On Thu, 10/1/19, Justin Lemkul <jalemkul at vt.edu>
 wrote:
 >
 >   Subject:
 Re: [gmx-users] RMSD plots protein-peptide complex
 >   To: gmx-users at gromacs.org
 >   Date: Thursday, 10 January, 2019, 4:19
 PM
 >   
 >   
 >   
 >   On 1/10/19
 6:31 AM, Dr. Seema Mishra wrote:
 >  
 >
 >   > Thanks Justin.
 >   > Are these two commands for RMSD OK
 after
 >   making index groups for
 protein only? Forgive my
 >  
 silliness:
 >   > gmx trjconv -s
 md_0_1.tpr -f
 >   md_0_1.xtc -n
 index.ndx -o md_0_1_noPBC.xtc -pbc mol -ur
 >   compact
 >   >
 Select 0
 >   >
 > 
  > gmx rms -s md_0_1.tpr
 >   -f
 md_0_1_noPBC.xtc -n index.ndx -o rmsd.xvg -tu ns
 >   >
 >   >
 Select 4 4 for
 >   backbone atoms. I
 think then GROMACS will recognize only the
 >   index groups will be used for
 identifying backbones
 >   >
 >   
 >   Sure,
 >   GROMACS does what you tell it. If you
 choose the default
 >   group 4
 >   (Backbone), it will consider all
 >   atoms that qualify as backbone,
 >   encompassing any protein in the system.
 What
 >   you need to do is create an
 >   index group
 >  
 with only the relevant atoms of the protein receptor (not
 >   
 >   the peptide
 ligand) and use that group for
 >  
 analysis. The mere presence
 >   of a
 >   protein-only index group will do
 nothing for you; you need
 >   to
 >   actually use it.
 > 
  
 >   -Justin
 >  
 
 >   >
 >   > 
    On Wednesday, 9
 >   January, 2019,
 8:30:52 PM IST, Justin Lemkul <jalemkul at vt.edu>
 >   wrote:
 >   >
 >   >
 >   >
 >   > On 1/9/19 6:07 AM,
 >   Dr. Seema Mishra wrote:
 >   >> Hello
 >  
 >> Any idea how to generate RMSD plots
 >   for only the protein in a
 protein-peptide complex? I mean,
 >   do
 give me commands for using only the protein backbone
 >   atoms as the g_rmsd uses all backbone
 atoms of peptide as
 >   well and I do
 not want peptide RMSD plots included.
 > 
  > Make an index group that includes only the
 >   atoms you want to analyze.
 >   >
 >   >
 -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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 --
 
 ==================================================
 
 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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