Re: [AMBER] Simple normal mode analysis in amber

From: David Case <>
Date: Sat, 7 Jan 2017 18:09:10 -0500

On Sat, Jan 07, 2017, Ella Gale wrote:
> 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
> grateful.

It is indeed a very short program to compute normal modes. See examples


There is also a complete example in Section 40.4 of the Amber 2016 Reference
Manual (entitled "Second derivatives and normal modes.") OK, this is 17
lines, but this example reads in the molecule information, carries out the
minimization, and then computes the normal modes (on line 17). So only one
line of code is really involved in computing normal modes.

For a more realisitic example:


(you will have to add a call to nmode() to the nab program in the second

...hope this helps....dac

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Received on Sat Jan 07 2017 - 15:30:03 PST
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