Never mind. I used editconf before the energy-minimisation on vacuum (specifying the size-box) and now, when i used genbox on the ’new’ structured it worked :D
-- Carlos Navarro Retamal Bioinformatic engineer Ph.D(c) in Applied Science, Universidad de Talca, Chile Center of Bioinformatics and Molecular Simulations (CBSM) Universidad de Talca 2 Norte 685, Casilla 721, Talca - Chile Teléfono: 56-71-201 798, Fax: 56-71-201 561 Email: carlos.navarr...@gmail.com or cnava...@utalca.cl On Wednesday, July 2, 2014 at 8:56 PM, Carlos Navarrro Retamal wrote: > Dear gromacs users, > I’m following this tutorial -> > http://md.chem.rug.nl/cgmartini/index.php/proteins > in order to performed a CG simulation of an specific protein in a water box. > My problem is that when i’m trying to solvate my protein with genbox, by > using the next command: > > > genbox -cp COR15A_CG-box.gro -cs water-box-303K-1bar.gro -vdwd 0.21 -o > > COR15A_CG-solvated.gro > > > > > > > The water box is placed next to the protein instead of surrounding it-> > http://cl.ly/1U2F1H3y3n2w. > I used the following command to center my protein before i used genbox, > without luck :/ > > > editconf -f COR15A_CG.pdb -center 0 0 0 -o COR15A_CG-box.gro -c -d 2.0 -bt > > cubic > I’m just start by using a CG representation of biological systems, so any > help will be welcome. > Have a nice day, > Carlos > > > -- > Carlos Navarro Retamal > Bioinformatic engineer > Ph.D(c) in Applied Science, Universidad de Talca, Chile > Center of Bioinformatics and Molecular Simulations (CBSM) > Universidad de Talca > 2 Norte 685, Casilla 721, Talca - Chile > Teléfono: 56-71-201 798, > Fax: 56-71-201 561 > Email: carlos.navarr...@gmail.com (mailto:carlos.navarr...@gmail.com) or > cnava...@utalca.cl (mailto:cnava...@utalca.cl) > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to gmx-users-requ...@gromacs.org (mailto:gmx-users-requ...@gromacs.org). > > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
