[gmx-users] Strange output with Genbox

mark.abraham at anu.edu.au mark.abraham at anu.edu.au
Wed Feb 13 14:34:34 CET 2008

----- 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):
> Output after genbox:

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.

> 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


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