[gmx-users] Strange output with Genbox

[Jens Pohl]

> ----- Original Message -----
> From: Jens Pohl <Pohl.Jens at web.de>
> Date: Thursday, February 14, 2008 12:25 am
> Subject: [gmx-users] Strange output with Genbox
> To: gmx-users at gromacs.org
> 
> > Hello!
> > 
> > I try to simulate a modified protein in a water-box. When I use 
> > genbox and have a look on the output-file then the water 
> > molecules are located in between the AA-sequence which results 
> > in an "exploding" molecule during the mdrun. I've done it 
> > several times from the very beginning, always getting a similar 
> > result (distribution of water in the AA sequence varied a bit). 
> > 
> > Input-sequence (AA):
> > MGVLAI...
> > 
> > Output after genbox:
> > OMOGOOVOLOAOIOO...
> 
> It's not easy to be sure exactly what you're describing here, but I think you mean that genbox is placing waters inside the expected vdW surface of your protein. If so, then check out "genbox -h" for how GROMACS works out this surface. Otherwise, please consider posting a picture to a website somewhere.

The water is placed in between the chain. When I have a look at the sequence there is water followed by AA followed by water. I've done a similar simulation before and there the sequence was Protein first and the the water residues.  

> > Commands used (copied from .bash_history):
> > pdb2gmx -f 165_in.pdb -p 165 -o 165 -n 165 -i 165 -q 165_out.pdb
> > 
> > (used ffG53a6)
> > 
> > editconf -f 165 -o CbzE_ec.pdb -bt cubic -vol -d 1.0 
> > 
> > genbox -cp 165_ec.pdb -cs ../Water.gro -o 165_gb.pdb -p 165_gb
> 
> Mark
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> 

Jens

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