AMBER Archive (2009)

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

From: Jason Swails (jason.swails_at_gmail.com)
Date: Fri Oct 16 2009 - 10:02:35 CDT

Frank,

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.

-Jason

2009/10/16 "Frank X. Vázquez" <fxv_at_umich.edu>

> 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
> fxv_at_umich.edu
> PhD Candidate
> Geva Group
> Chemistry Department
> University of Michigan
>
>
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
> 

-- 
---------------------------------------
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
  • application/x-sh attachment: scan.sh

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