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 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 <[email protected]> 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 | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > _______________________________________________ > gmx-users mailing list [email protected] > 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 [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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