I want to measure the average RMSD value of my protein but only limit to the residues within 5A of targeted residue. Is that possible?
For example:
Residues within 5A of residue K66
= W64, N65, A67, S68, F181 and D182
Should I make the custom index first? But how?
Can anyone help me by giving me the command please?
I'm kinda new to gromacs. Still learning.
Thank you.
RMSD of single amino acid doesn't make a sense. You have yo consider to calculate RMSF for each amino acid. gmx rmsf -f .. -s .. -res . It helps you to obtain residual fluctuations of your protein.
You have to make a index file where you make index (gmx make_ndx) for your desire residues group. Then just run RMSD command using that index file and during selection use your group to calculate RMSD.
Hello Mohd,
If you don't know your way around GROMACS, I suggest using other freely available tools like the SPDBV or online servers like the TM-align by Zhang lab. The server could be accessed using the following link:
https://zhanglab.ccmb.med.umich.edu/TM-align/
Hope this helps!
- Badges
- Science topic