17 Jan
2008
17 Jan
'08
4:05 p.m.
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: 23 1.264 which is the frame number and the RMSD. --Eric