Thank you, Justin. Your online tutorial helped me a newbie a lot. I ever tried using genbox -ci -nmol to insert two proteins in a specific box. But it didn't work. Nothing was inserted into the box. Maybe enlarging the box would work. I would try.
On Mon, Apr 1, 2013 at 10:21 AM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 3/31/13 9:51 PM, Zhikun Cai wrote: > >> Hi everyone, >> >> I am trying to insert two same proteins in a simulation box. Now I have >> used pdb2gmx to convert one protein's pdb file to gro file. Then how >> should >> I do? How could they be randomly positioned and oriented in the box? >> > > Place them however you like within the box using editconf -center, > -translate, -rotate, etc as necessary. You may be able to get completely > random insertion with genbox -ci -nmol, but I've never tried it with a > protein. > > -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
