[gmx-users] RMSD plots protein-peptide complex

[Justin Lemkul]

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

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