sunny mishra wrote:
oh cool. I have gromacs version 4.4 so my protein will be on the x
axis by default and to orient the long axis of protein along z axis
then I have to editconf it and then rotate the final structure to 90
degrees along y axis, right? reply will be highly appreciated
Try it and see. You learn more by doing, and anyway, it takes about 10 seconds
to run editconf, instead of waiting for a reply seeking affirmation.
-Justin
Thanks,
Sunny
On Sun, Oct 18, 2009 at 10:18 PM, Justin A. Lemkul <jalem...@vt.edu> wrote:
sunny mishra wrote:
Dear All,
I am following the tutorial given by justin and have question
regarding the orientation of protein. Tutorial says that orient the
protein along z axis using editconf -princ command followed by the
rotation along y axis. My question is that when I use the editconf
-princ command, does it automatically orient the protein along z axis
because i gave the following command and I wasn't sure if I am correct
or not, the command is: editconf -f protein.gro -princ -o
protein_z.gro
It depends on your Gromacs version. As stated in the tutorial:
"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. If you want to
skip the construction of this peptide, the properly oriented structure can
be found here."
Please correct me if I am wrong and also what do you mean when you say
followed by the rotation along the y axis, by how much angle do i need
to rotate?
What angle do the coordinate axes make with one another? :)
-Justin
Thanks,
Sunny
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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