[gmx-users] Strange output with Genbox

[Jens Pohl]

> -----Ursprüngliche Nachricht-----
> Von: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Gesendet: 13.02.08 14:27:25
> An: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Betreff: Re: [gmx-users] Strange output with Genbox


> 
> Jens Pohl wrote:
> > 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...
> > 
> > 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
> > 
> 
> What is in ../Water.gro? It should be pure water.

Water.gro is my renamed SPC water from the GROMACS package.

> 
> What system are you running on?
Simple Pentium IV-system with which I've done some simulations before.

> 
> > 
> > Thank you very much in advance for your suggestions to solve the problem
> > Jens
> > 

Jens
_____________________________________________________________________
Der WEB.DE SmartSurfer hilft bis zu 70% Ihrer Onlinekosten zu sparen!
http://smartsurfer.web.de/?mc=100071&distributionid=000000000066