[gmx-users] Re: GPCR MD Tutorial Using GROMACS (URL)

[Anirban Ghosh]

Hello Bala,

Yes, exactly as Justin said it represents just a workflow where a GPCR
protein (here B2AR) has been taken as an example. I mentioned it as a GPCR
tutorial because many often inquire about GPCR MD simulations only in the
forum. But it can be adapted for other membrane proteins as well. And
secondly again as Justin mentioned, the choice of lipid depends upon the
system you wish to replicate.

Regards,

Anirban

On Thu, Apr 26, 2012 at 11:10 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 4/26/12 9:35 AM, Bala S wrote:
>
>> Dear Anirban,
>>
>> Thanks for the tutorial you have created for the newbies like me to
>> follow.
>>
>> I wonder the tutorial is only for the GPCRs not applicable for other
>> membrane proteins?
>>
>>
> Tutorials present possible workflows.  Anirban's tutorial does not
> significantly differ from my own (linked from his) which I happen to know
> has been applied to many different systems.  There is nothing GPCR-specific
> in this new tutorial, just like there is nothing KALP-specific about mine.
>
>
>  I also have another question about slecting a lipidbilayer, what is the
>> criteria is selecting it, for instance popc, dopc or dppc?
>>
>>
> The choice of lipid depends on what you need to model.
>
> -Justin
>
> --
> ==============================**==========
>
> Justin A. Lemkul
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> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
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