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
<jalem...@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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