[gmx-users] Strange output with Genbox

[Jens Pohl]

> ----- 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


The topology seems to be ok. The only difference between editconf and genbox is the number of solutes.
So it might be just a problem with the depiction of the system combined with unsufficient EM? I'll try it, hope the best and report the results. 

Thank you very much
Jens
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