From: Evandro Semighini (
Date: Wed Nov 04 2015 - 07:08:34 CST


I ran a set of MDs of docking results, using AMBER Force Fields and NAMD,
and now I am facing some issues to get the RMSD of the docked molecules.

I am not being able to use the residue_rmsd.tcl script. When I select "not
protein and not water", at the "set sel_resid" phase, it shows me the
number of the residue concerning the docked molecule, but when I run
"rmsd_residue_over_time top $sel_resid", it says that no atom was selected.

The RMSD Trajectory Tool, using the "# resid XX" comment, doesn't seem to
show the right result, or, as the numbers are diferent of those I get with
the "print_rmsd_through_time" and doesn't change if I change the number at
the comment.

I used the print_rmsd_through_time script and got interesting results, but
the tk console seems to be limited to 500 lines, and I have 5000. I am not
being able to save this whole history of the console.

Can you help me to see where I am missing, please?

Thank you in advance.

Evandro Semighini