On Jan 16, 2008, at 8:19 AM, Francesco Pietra wrote:

I was unable to find how to get a plot of RMSD against time. I would like to do

that for the ligand (which is a single big residue) and selected residues of

the protein.

Mmmm, RSMD compared to what? Frame 1?

You can't get such a plot right now, but what you can do is open your trajectory and also open a PDB file with whatever structure you want to measure RMSD with, and in the "Define script..." dialog put:

echo <FRAME>

match #0<+atom spec you wanted compared> #1<+atom spec you want compared>

Then if you play through the trajectory, in the reply log will be pairs of lines like this:

1.264

which is the frame number and the RMSD.

--Eric