[gmx-users] Tutorial

[Sara baretller]

HI

in the tutorial , it says that the script has the instructions to follow but
when i opened the script i didn't find any instructions

please what does 14 stands for and 5

perl inflategro.pl system.gro 4 DPPC 14 system_inflated.gro 5 area.dat


thank you






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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