[gmx-users] Tutorial

[Justin A. Lemkul]

Sara baretller wrote:
> 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 <http://inflategro.pl> system.gro 4 DPPC 14 system_inflated.gro 5 area.dat
> 

14 is a cutoff radius for deleting lipids.  5 is the grid spacing for the area 
measurement, if memory serves.  Both terms are in Angstrom.

-Justin

> 
> thank you 
> 
> 
> 
> 
> 
> 
> On Wed, Aug 17, 2011 at 4:19 PM, Sara baretller 
> <sarabiocomputation at gmail.com <mailto: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 <mailto:sarabiocomputation at gmail.com>>
>     wrote:
> 
>         Thank you
> 
>         yes i removed the Remove unnecessary lines ... i found the
>         inflategro.pl <http://inflategro.pl/>
>         when i click on the rl inflategro.pl <http://inflategro.pl/>  it
>         gives me Firefox can't find the server at inflategro.pl
>         <http://inflategro.pl>.
> 
> 
> 
> 
> 
>         <http://inflategro.pl/>
>         On  Wed, Aug 17, 2011 at 3:17 PM, Justin A. Lemkul
>         <jalemkul at vt.edu <mailto: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>
>                 <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 <http://vt.edu> | (540) 231-9080
>             <tel:%28540%29%20231-9080>
> 
>             http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin
>             <http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
> 
>             ==============================__==========
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> 

-- 
========================================

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

========================================