[gmx-users] Protein Orientation

[sunny mishra]

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

Thanks,

Sunny

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
>> 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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