Re: [AMBER] Simple normal mode analysis in amber

From: Huang Jing <>
Date: Sat, 7 Jan 2017 22:18:53 +0200

Build the pdb file for your molecules and then generate the parameter by
using "antechamber" command in Ambertool;
then the parameters of bond stretching, angle stretching,... would be
listed in the .frcmod file;
here is the tutorial for "antechamber"


On Sat, Jan 7, 2017 at 7:15 PM, Ella Gale <> wrote:

> 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
> grateful.
> 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.
> Regards
> Ella
> _______________________________________________
> AMBER mailing list
AMBER mailing list
Received on Sat Jan 07 2017 - 12:30:02 PST
Custom Search