[gmx-users] RMSD plots protein-peptide complex

[Dr. Seema Mishra]

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



   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

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Justin A. Lemkul, Ph.D.
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