[gmx-users] Tutorial

[Sara baretller]

ok i did find the script

thank you



On Wed, Aug 17, 2011 at 4:03 PM, Sara baretller <
sarabiocomputation at gmail.com> wrote:

> 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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>
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