[gmx-users] orientation of helical peptide

Louic Vermeer science at louic.nl
Sat Sep 10 20:42:41 CEST 2005

Dilraj Lama wrote:
> hello gmx-users,
>                 I have two helical peptide of 16 residues each.I want to orient these peptides
> parallel to each other in one case and perpendicular to one another in another.How
> can I do this using Gromacs?
> Please suggest.
> Thank you.

I would suggest to use a visualisation program like molmol or VMD to do 
the job. You could just drag & drop the helices roughly the way you want 
It might however be "more scientific" to write a script to do the job, 
but it could be that you don't need that kind of accuracy.

Have fun!

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