[gmx-users] Strange output with Genbox

[mark.abraham at anu.edu.au]

----- Original Message -----
From: Jens Pohl <Pohl.Jens at web.de>
Date: Thursday, February 14, 2008 5:56 pm
Subject: Re: [gmx-users] Strange output with Genbox
To: Discussion list for GROMACS users <gmx-users at gromacs.org>

> > ----- 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.  

Genbox doesn't change your solute topology, so it is certainly not changing your sequence.

Mark