AMBER Archive (2006)

Subject: AMBER:

From: Steve Seibold (
Date: Wed Sep 20 2006 - 11:56:00 CDT

Hello Amber

I have been attempting to get RMSD per RESIDUE and RMSF per RESIDUE
using AMBER8. I have attached the files containing my script for ptraj.
My RMSd vs. time and RMSF vs time do indeed show a drastic difference
between their values throughout the time frames. However my RMSD_RESIDUE
and RMSF_RESIUDE show no difference at all in their values. They both
give me two RMSF values. That is, there is no RMSD per residue. It
appears as if "atomifluc", even when I fit frames to the crystal pdb,
gives me the fluctuation around a "positioned-averaged" structure. I am
not sure where this average structure is coming from, but it must be
calculating it from the mdcrd files???


I repeated the calculations in another software package and it revealed
that the RMSD_RESIDUE and RMSF_RESIUDE graphs are drastically different.
So I must be doing something incorrect with the above input files, but I
cannot figure it out.


Can someone please assist me?


Thanks, Steve

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