[AMBER] Normal Model Analysis with AmberTools20

From: Harley Wilson <hyw4988.rit.edu>
Date: Wed, 9 Sep 2020 19:09:46 -0400

Good afternoon,

Hello! My name is Harley Wilson and I am a research student at RIT working
on using Normal Mode analysis with AmberTools20. I have attempted to follow
older tutorials available on the website, but they have not worked with my
protein (PDB 4EZI). I have also looked at the 2020 manual and see that
there is a line of code for completing the analysis in a streamlined
manner. I use the Ubuntu20 system and downloaded AmberTools20 through

With the manual, I do not understand these lines of code and what they do
(pg. 839):
 $ molecule m
 $ float x[4000], fret

I also receive an error when inputting these. Could anyone explain this and
the best way to approach normal mode analysis?

Harley Wilson
Rochester Institute of Technology, BS Biochemistry (Projected in 2021)
AMBER mailing list
Received on Wed Sep 09 2020 - 16:30:03 PDT
Custom Search