Hi Bing, You do want to use genconf for that (the way you use it, editconf scales the coordinates).
genconf -f xxx.pdb -nbox 2 2 1 -o zzz.pdb The thing to make sure is that all molecules are whole before processing them with genconf. The other possibility is to use editconf to translate a few copies of your system and then stitch these fiels together. But genconf is quicker and more convenient. Cheers, Tsjerk On Tue, Jul 7, 2009 at 7:26 AM, Bing Bing<jarbin...@gmail.com> wrote: > Dear all, > I want to extend the membrane into 512 POPC with the starting structure of > 128 POPC. I 've used :- > editconf -f xxx.pdb -scale 2 2 1 -o zzz.pdb. > I noticed that the pdb file that generated by editconf have only 1 set of > 128 popc. Using vmd, the extended structure is in pieces, the no bond > between each atom. When i checked the pdb file, i didn't find any atomic > coordination for the extended set of POPC. Did i missed out anything here? > or what I've done is wrong here? > > When i used genconf , the extended structure looks fine. But, i found some > discussion regarding genconf whereby the structure will not be in one pieces > if this command is used. Please advice. > > Thank in advance. > > > Regards, > bing > > _______________________________________________ > gmx-users mailing list gmx-us...@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 > -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 _______________________________________________ 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