No. But in order to do that with lipid.gro what co-ordinates should I have to take?
On Thu, Oct 29, 2009 at 4:40 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > sunny mishra wrote: > >> okk...here are the commands which I am givng... >> >> editconf -f 1SU4_cleancg_trans.gro -o 1SU4_newbox.gro -c -box 13.29820 >> 13.29820 6.59160 >> >> I get the 1SU4_newbox.gro which has co-ordinates 13.29820 13.29820 6.59160 >> >> > Have you done the same with lipid.gro? If the protein and the lipid are in > different coordinate systems (i.e., lipid.gro centered at the origin and > protein centered within the box, which has its corner placed at the origin) > then you will have a problem. > > -Justin > > cat 1SU4_newbox.gro lipid.gro > system..gro >> >> Now here system.gro also has co-ordinates 13.29820 13.29820 6.59160 >> >> now inflategro: >> >> inflategro system.gro 4 DSPC 14 -o inflated_bilayer.gro 5 >> >> Now when i visualize my output file in VMD then protein and lipid are >> seperated and even after i scale it to .95 they dnt meet....they are still >> apart, I was hoping that lipid will be scaled and protein shud have remained >> in the center of the lipid but that doesn't happen. I hope you got my >> question >> >> On Thu, Oct 29, 2009 at 4:25 PM, Justin A. Lemkul <jalem...@vt.edu<mailto: >> jalem...@vt.edu>> wrote: >> >> >> >> sunny mishra wrote: >> >> Yes I did the same and when I see my system.gro file it gives me >> the dimensions of the protein box half of the lipid bilayer box >> so that means it should now be set in the center of the lipid >> bilayer. But after >> >> >> I don't understand what you mean. >> >> >> that when I run the inflategro script and see my output file the >> protein and lipid are separated and I dnt know why? >> >> >> Can you post the actual commands you're using? >> >> -Justin >> >> >> -- ======================================== >> >> Justin A. Lemkul >> Ph.D. Candidate >> ICTAS Doctoral Scholar >> Department of Biochemistry >> Virginia Tech >> Blacksburg, VA >> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080 >> >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> ======================================== >> _______________________________________________ >> gmx-users mailing list gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org> >> >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/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 >> <mailto:gmx-users-requ...@gromacs.org>. >> >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> >> >> > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > 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 > Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php >
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