[gmx-users] Tutorial

[Sara baretller]

Thank you

yes i removed the Remove unnecessary lines ... i found the inflategro.pl
when i click on the rl inflategro.pl  it gives me Firefox can't find the
server at inflategro.pl.





<http://inflategro.pl/>
On  Wed, Aug 17, 2011 at 3:17 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> Sara baretller wrote:
>
>> I am doing the protein in lipid tutorial . http://www.bevanlab.biochem.**
>> vt.edu/Pages/Personal/justin/**gmx-tutorials/membrane_**
>> protein/02_topology.html<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/02_topology.html>
>>
>> Pack the lipids around the protein, i dont see where is the script perl
>> inflategro.pl <http://inflategro.pl>
>>
>>
>> I googled It and did not find it. Can you please send me the script or
>> tell me where I can find it
>>
>>
>>
> Then Google again :)  If you search "Inflategro" it is the first result
> that comes up.
>
>
>  Also I used the cat KALP_newbox.gro dppc128_whole.gro > system.gro
>>
>> so I checked the system.gro in vmd and did not load anything. I was able
>> to vew the KALP_newbox.gro and the dppc128_whole.gro but not the system.gro
>>
>> do I have to organize the system.gro because I can see that the protein in
>> numbered from 1 to … then the lipids start from 1 ….end .. will that cause a
>> problem
>>
>>
> Numbering is irrelevant.  You probably didn't clean up the file as
> instructed in the tutorial:
>
> "Remove unnecessary lines (the box vectors from the KALP structure, the
> header information from the DPPC structure) and update the second line of
> the coordinate file (total number of atoms) accordingly."
>
> -Justin
>
> --
> ==============================**==========
>
> Justin A. Lemkul
> Ph.D. Candidate
> 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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