[gmx-users] Tutorial

[Justin A. Lemkul]

Sara baretller wrote:
> 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 
> 

Then the file format is still broken in some way.

-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

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