[gmx-users] Tutorial

Justin A. Lemkul jalemkul at vt.edu
Wed Aug 17 21:17:37 CEST 2011

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
> 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 A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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