maximos 发表于 2021-6-24 04:54
Thank you All very much for your valuable answers,
During my searching in the same subject, I found ...

if you want to use this method,In VMD,you can choose "Extension"-"Analysis"-"RMSD Trajectory Tools".Then choose the residues you want to calculate.After choose the proper parameters,press "Align" and "RMSD".Besides,you can also use "Extension"-"Analysis"-"Timeline".
You also can do it through Gromacs,it's recommended to read the manual.

As mentioned in #2, you can perform several nanoseconds MD simulation, and then calculate RMSF of each residue in the possible binding region. The residue with relatively large RMSF is usually flexible , and may need to be set to be flexible in your docking code.

If you can understand Chinese ,it's recommended to read the article of Sobereva:
http://sobereva.com/32

you can try this:
gmx rmsf -f XXX.xtc -s XXX.tpr -o rmsf_protein.xvg -oq bfac.pdb -res -b A
XXX is the name of your files,A is the start frame of sampling for calculating RMSF and Beta Factor.
the Beta Factor,which is derived from rmsf,is a way to perform the flexibility of the protein.
you can import bfac.pdb into VMD ,choose "Beta" as Coloring Method,then you can get the the flexibility of residues visually.