[gmx-users] Solvating protein in a CG representation - genbox problem

Carlos Navarrro Retamal cnavarro at utalca.cl
Thu Jul 3 03:02:05 CEST 2014

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 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.navarro87 at gmail.com or cnavarro at utalca.cl

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