[gmx-users] Strange output with Genbox
Pohl.Jens at web.de
Wed Feb 13 14:30:19 CET 2008
> -----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
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