Hi,

It is possible to calculate RMSD of certain region of a protein using cpptraj software, the executable cpptraj and cpptra.MPI are available in the AMBER bin directory.

An exemple of cpptraj script :

######################

parm topology.prmtop # The name of the prmtop file

trajin tajectory.(nc,mdcd, dcd etc) # The name of your trajectory file

reference reference.pdb ## or reference.rst AMBER pdb or restart

rms reference : first residue -last residue out rmsd.out ## (The output file )

######################

As Akli said, you can calculate RMSD values using cpptraj. And, you can choose the certain region using 'mask' (see the AMBER manual, cpptraj part). In the case of protein backbone, CA, C, N, and O can be the mask atoms. Sometimes, only CA is used to represent a motion of backbone.

Hello, all.

Thank you for your kind replies.

Thanks to your advice, I could perform what I want to do.

I really appreciate to your help.

By the way, I could do with the script as below.

#####################################

trajin

reference

rms reference @N,CA,C

rms reference nofit out

#####################################