[gmx-users] Tutorial

[Sara baretller]

Hi so i did

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. After i  use the

cat KALP_newbox.gro dppc128_whole.gro > system.gro


when i check the file system.gro it has the protein and the lipid
coordinates,  however when i load to vmd to veiw , the VMD does not
show anything , does any body have an idea what s wrong

Thank you


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> On Wed, Aug 17, 2011 at 4:19 PM, Sara baretller <
> sarabiocomputation at gmail.com> wrote:
>
>> 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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