AMBER Archive (2009)

Subject: Re: [AMBER] Dihedral energy profile in a single molecule

From: Jason Swails (
Date: Fri Oct 16 2009 - 10:02:35 CDT


I use nmr restraints on the dihedral and change the value that i restrain
the dihedral to.

I'll attach a bash script i created a while ago to do this. You'll have to
edit the header of the script with your prmtop/inpcrd files and what kind of
resolution you want, but hopefully it'll work.


2009/10/16 "Frank X. Vázquez" <>

> Hello Amber users,
> How does one calculate the energy profile for a given dihedral angle in a
> single molecule? I would like to create an energy profile of one of the
> dihedral angles in an isolated molecule of hexatriene in order to compare
> the GAFF with electronic structure calculations.
> Thank you,
> Frank Vázquez
> --
> Frank X. Vázquez
> PhD Candidate
> Geva Group
> Chemistry Department
> University of Michigan
> _______________________________________________
> AMBER mailing list

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student

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