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

Thomas Lipscomb linuxborg2 at yahoo.com
Sat Nov 8 03:35:50 CET 2014

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."


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.



PS: yes I looked at the GROMACS manual
Page 13
The program editconf produces the orientation which has a square intersection with the xy-plane.
Page 171
gmx editconf -translate 0 0 <l_z>, where l_z

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