[gmx-users] Strange output with Genbox
Pohl.Jens at web.de
Thu Feb 14 09:07:54 CET 2008
> ----- 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.
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
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