[AMBER] RMS2D maybe?

From: Fabrício Bracht <fabracht1.gmail.com>
Date: Sun, 17 Nov 2013 17:06:33 -0200

Hi, I have a protein which is a homo-dimer, i.e., subunit A is identical in
sequence to subunit B. I would like to know how each structure evolve
relative to the other one during md. Actually I only want to analyze 8
residues from the active site. The manual states that rms2d calculates the
rms of each frame to each other frame. That means that I'll have a
comparison between frame 1 and all the other frames individually, frame 2
and all the others....etc, right? But does that mean that I can calculate
the rms of frame 1 for Residues 1,2,3 using as reference residues A,B,C for
all the other frames. Is this the proper way to do this type of analysis?
I've tried:

rms2d Sitio :202,204,206,257,259,260,261,264.C,CA,N rmsout rmsd-sitio.gnu
refttraj mdcrd.md2 :31,33,35,86,88,89,90,93.C,CA,N

and got a very nice and colorful graphic, but I am not really sure that
group 1 of residues were analyzed against group 2.
Thank you
AMBER mailing list
Received on Sun Nov 17 2013 - 11:30:03 PST
Custom Search