[gmx-users] RMSD plots protein-peptide complex

[Dr. Seema Mishra]

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?

--------------------------------------------
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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