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 system.gro 4 DPPC 14 system_inflated.gro 5 area.dat thank you On Wed, Aug 17, 2011 at 4:19 PM, Sara baretller < sarabiocomputat...@gmail.com> wrote: > 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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