[gmx-users] Solvating protein

[Mark Abraham]

On 10/07/2010 1:28 AM, Sai Pooja wrote:
>
> Hi,
>
> When I start from a energy minimized protein in vacuum and solvate it 
> using genbox, the output message says that the protein has zero 
> charge. So I skip the genion step. I follow this with energy 
> minimization of the solvated protein followed by restraining the 
> protein and then doing a short mdrun (as is the usual procedure 
> outlined in most tutorials). However, when I run the grompp command as 
> the first step for the position restrained md, it runs but prints a 
> note saying that the system has non-zero charge ~ -  0.9999.
>
> NOTE 2 [file finalnoss.top, line 8070]:
>   System has non-zero total charge: -9.999994e-01
>
> I dont understand. Do I need to run the genion step anyway or is it 
> okay to continue with this system?

I'd believe grompp before genbox. Surely you know already what is in 
your system, and thus its total charge. You should already know the 
protonation state of all of your relevant protein residues, because you 
made choices for them with pdb2gmx.

Mark

>
> Pooja
>
> -- 
> Quaerendo Invenietis-Seek and you shall discover.
>
>
>
> -- 
> Quaerendo Invenietis-Seek and you shall discover.