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

Thomas Lipscomb linuxborg2 at yahoo.com
Sat Nov 8 20:48:54 CET 2014

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?

On Friday, November 7, 2014 9:40 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

On 11/7/14 9:29 PM, Thomas Lipscomb wrote:
> Dear Gromacs mailing list,
> I fixed my problem with dangling bonds by adding the two appropriate charged ends.
> But I also need to orient my protein along an axis to get ready to insert it across a membrane to see how it disrupts the membrane.  The tutorial that I am working with wants it oriented along the z-axis.
> "The .pdb file was oriented along the z-axis using editconf -princ, followed by a rotation about the y axis. Note that in GROMACS-3.3.x, the -princ option oriented the long axis of the structure (in this case, the helix axis) along the z-axis by default, but this option has changed as of GROMACS-4.0.4, which orients the long axis along the x-axis."
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/01_pdb2gmx.html
> Here is my best guess at the appropriate command for gromacs-5.0.1:
> /usr/local/gromacs/bin/gmx gmx editconf -princ
> But because this is 5.0.1 then -princ orients along the x-axis not the z-axis that I need.

So, as the tutorial says, you need to follow that up with a rotation about the 
y-axis, which is where editconf -rotate comes in handy.



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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