[gmx-users] Orienting a protein along an axis in GROMACS

Justin Lemkul jalemkul at vt.edu
Sat Nov 8 21:18:17 CET 2014

Please keep the discussion on the mailing list.

On 11/8/14 3:11 PM, Thomas Lipscomb wrote:
> The protein is a linear alpha helix that will be aligned on the x-axis by
> -princ.  So the protein will be 90 degrees to both the Y and Z axes before
> -rotate.  So what should Y be?

You just answered your own question.  If you have the structure aligned along 
one axis, and you want it aligned along another, you rotate by 90 degrees around 
the third axis.  All Cartesian axes are 90 degrees from one another.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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