Alright. I have done this....I have made another lipid_newbox.gro file and wrote same box vectors as of lipid.gro file
For LIPID : editconf -f lipid.gro -o lipid_newbox.gro -c -box 13.29820 13.29820 6.59160 For Protein : editconf -f protein.gro -o protein_newbox.gro -c -box 13.29820 13.29820 6.59160 Then cat the system and made system.gro file and did inflategro of the system.gro file. Do you think this is the correct way and now when I visualize this in VMD the protein is shifted little upwards but it is at the center of the lipid. Sunny On Thu, Oct 29, 2009 at 4:59 PM, Justin A. Lemkul <[email protected]> wrote: > > > sunny mishra wrote: > >> No. But in order to do that with lipid.gro what co-ordinates should I have >> to take? >> >> > I think you need to differentiate between "coordinates" and "box vectors." > You should center the molecule in the box (defined by the vectors in the > last line of the .gro file). I assumed you were specifying these box > vectors with -box. > > So, for both the protein and the lipid coordinate files, you need to use > > editconf -c -box (x, y, z from .gro file) > > -Justin > > On Thu, Oct 29, 2009 at 4:40 PM, Justin A. Lemkul <[email protected]<mailto: >> [email protected]>> 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 >> <[email protected] <mailto:[email protected]> >> <mailto:[email protected] <mailto:[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 <http://vt.edu> <http://vt.edu> | (540) >> >> 231-9080 >> >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> ======================================== >> _______________________________________________ >> gmx-users mailing list [email protected] >> <mailto:[email protected]> >> <mailto:[email protected] <mailto:[email protected]>> >> >> >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/searchbefore >> posting! >> Please don't post (un)subscribe requests to the list. Use the >> www >> interface or send it to [email protected] >> <mailto:[email protected]> >> <mailto:[email protected] >> <mailto:[email protected]>>. >> >> 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 <http://vt.edu> | (540) 231-9080 >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> ======================================== >> _______________________________________________ >> gmx-users mailing list [email protected] >> <mailto:[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] >> <mailto:[email protected]>. >> 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 [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 >
_______________________________________________ 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
