[gmx-users] Tutorial

[Peter C. Lai]

The author of InflateGRO, Christian Kandt, is now at Univ. of Bonn.
All his work is here: http://www.csb.bit.uni-bonn.de/inflategro.html

On 2011-08-17 03:03:50PM -0500, Sara baretller 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
> 
> 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
> 
> ========================================
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==================================================================
Peter C. Lai			| University of Alabama-Birmingham
Programmer/Analyst		| BEC 257
Genetics, Div. of Research	| 1150 10th Avenue South
pcl at uab.edu			| Birmingham AL 35294-4461
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