ok i did find the script thank you
On Wed, Aug 17, 2011 at 4:03 PM, Sara baretller < sarabiocomputat...@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 <jalem...@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> >> >> ==============================**========== >> -- >> gmx-users mailing list gmx-users@gromacs.org >> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> >> Please search the archive at http://www.gromacs.org/** >> Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before >> posting! >> Please don't post (un)subscribe requests to the list. Use the www >> interface or send it to gmx-users-requ...@gromacs.org. >> Can't post? Read >> http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >> > >
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