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

[Carlos Navarrro Retamal]

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.navarro87 at gmail.com or cnavarro at 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.navarro87 at gmail.com (mailto:carlos.navarro87 at gmail.com) or cnavarro at utalca.cl (mailto:cnavarro at utalca.cl)
>  
> --  
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