Dear Justin, Thanks a lot. I used this and it works fine:
editconf -f final.pdb -o final.gro -c -d 0.0 regards, Jiomm On Sat, Jun 15, 2013 at 3:09 AM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 6/14/13 8:08 PM, gromacs query wrote: > >> Dear Justin, >> >> I saw your tutorial ( >> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin/** >> gmx-tutorials/membrane_**protein/03_solvate.html<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/03_solvate.html> >> >> ) >> >> But my case is different. I can not even generate tpr file (trjconv as >> tutorial says) as it need box info >> >> Can you please suggest what can be the best possible way? If I just use >> system size dimension (X, Y Z) and do mimization it break my system in >> parts! >> >> >> How to choose optimum box vector in such case? >> >> > Omit "-bt cubic" from your command and it should work fine. > > > -Justin > > -- > ==============================**========== > > Justin A. Lemkul, Ph.D. > Research Scientist > 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> > -- 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/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
