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

[Justin Lemkul]

On 11/8/14 2:42 PM, Thomas Lipscomb wrote:
> Ok so then the command would be:
> /usr/local/gromacs/bin/gmx editconf -f model1.pdb -o model1_editconf.pdb -princ -rotate 0 Y 0
>
> I think Y would be some number of degrees to rotate the protein on the Y-axis.  What number should Y be?
>

What angle do the y- and z-axes form?

-Justin

-- 
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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
http://mackerell.umaryland.edu/~jalemkul

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