[gmx-users] RMSD plots protein-peptide complex

[Justin Lemkul]

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

==================================================