[gmx-users] orientation of helical peptide

Eric Jakobsson jake at ncsa.uiuc.edu
Sat Sep 10 22:29:25 CEST 2005

Pymol is another good visualization program for doing stuff like this.

At 01:42 PM 9/10/2005, you wrote:
>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 
>>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 them.
>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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Eric Jakobsson, Ph.D.
Professor, Department of Molecular and Integrative Physiology, and of 
Biochemistry, and of the Center for Biophysics and Computational Biology
Senior Research Scientist, National Center for Supercomputing Applications
Professor, Beckman Institute for Advanced Science and Technology
4021 Beckman Institute, mc251
University of Illinois, Urbana, IL 61801
ph. 217-244-2896       fax 217-244-2909

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