[gmx-users] Protein Orientation

[sunny mishra]

sure. thanks

On Sun, Oct 18, 2009 at 10:45 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> 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 <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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>>
>
> --
> ========================================
>
> 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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