[gmx-users] Protein Orientation
Justin A. Lemkul
jalemkul at vt.edu
Mon Oct 19 04:45:07 CEST 2009
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.
> On Sun, Oct 18, 2009 at 10:18 PM, Justin A. Lemkul <jalemkul at 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
>> 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? :)
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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
>> gmx-users mailing list gmx-users at gromacs.org
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Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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