Hi, all.

I am JunKoo and am quite new here.
I want to calculate the correlation between B-factor of original protein data(PDB file) and that of calculated data using normal modes.
So, I want to calculate rmsf for each atom using normal modes.

I used the vibran command and diag worked successfully.
and I am having hard time using rmsf-residue-str.

My questions is
1) Do I need to use rmsf-residue.str ? Is there any other way?

2) If I use rmsf-residue-str, how to choose and make trajectory in order to get traj.cor ?
Does rmsf depend on the trajectory that I choose ?

3) When I use dynamics.inp, I get the traj.cor
When I run charmm, I got the following error.

[jun@protein sample]$ charmm <rmsf1not.inp> rmsf1not.out
sue : unformatted io not allowed
apparent state: unit 90 named 1not.psf
lately reading sequential unformatted external IO

Thank you.

Last edited by Jun; 04/14/10 02:27 AM.