[AMBER] Simple normal mode analysis in amber

From: Ella Gale <ella.gale.gmail.com>
Date: Sat, 7 Jan 2017 17:15:45 +0000

Hi All,

I am trying to get the normal modes of simple chemicals (like hexane,
benzene) in vacuo. I've spent hours looking through the tutorials, the
internet and the manuals for both amber 2016 and 2015. I can see there is a
lot of information there and some mention of normal modes, but all I want
to do is take a structure built in leap, use a simple forcefield, minimise
it (I know how to do all those steps) and then calculate the normal modes
and output them to a file.

How should I do it? Which program is best? Does anyone have any example
code for this? I really expect it to be a two liner, so if anyone can give
me those two lines or point me in the right direction, I would be very

I really would appreciate any one helping me out.

And to the tutorial writers, can we please have a tutorial for doing such
simple chemical tasks on simple molecules please? Or a tutorial on
calculating normal modes.


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Received on Sat Jan 07 2017 - 09:30:02 PST
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