[gmx-users] Minimization problem, again!

[liu xin]

Hello Viswanadham and Andrea,

My protein is generated from our lab, I use dppc128 membrane.

After I use genbox to remove clashes, I use genbox again to solvate my
lipid/protein system in water, but when I do grompp there comes another
error:
##########################################################################
Fatal error: number of coordinates in coordinate file (merge.gro, 115120)
does not match topology (merge.top, 116570)
##########################################################################
I download the dppc128 top file from the websit, and generate the protein
top file by hand, then I make them as a whole top file for my lipid/protein
system, cause there's a error when I use pdb2gmx to generate a top file for
the whole system.
If I  choose to use the download top file for my bilayer, how can I solve
this problem?

Thanks in advance!

On 12/15/05, Viswanadham Sridhara <muta.mestri at gmail.com> wrote:
>
> Hi Andrea and Liu,
> Since you are discussing this topic, I have a general Question.
> 1.) What is the protein you are using( any ID of the protein to search in
> protein data bank), and
> 2) what kind of membrane is it?(DPPC, DOPC??)
> And how big is your initial membrane(128 , 256 or 512 lipids??).
> Thanks in advance,
> Viswam.
>
> On 12/15/05, andrea spitaleri <spitaleri.andrea at hsr.it> wrote:
> >
> > Hi Liu,
> > I explain it a bit better.  Basicaly I create my system protein/membrane
> > with vmd, not taking in account possible clashes. Afterwards, I use the
> > gromacs tools, genbox, in order to solvate the protein with the membrane as
> > well described here:
> > http://www.dddc.ac.cn/embo04/practicals/9_16.htm
> > genbox remove in such way eventual clashes.
> >
> > I hope this is a bit clearer
> >
> > Regards
> >
> > andrea
> >
> >
> > --
> > -------------------------------
> > Andrea Spitaleri
> > Dulbecco Telethon Institute
> > c/o DIBIT Scientific Institute
> > Biomolecular NMR, 1B4
> > Via Olgettina 58
> > 20132 Milano (Italy)
> > [image: Get Firefox!]
> > <http://www.spreadfirefox.com/?q=affiliates&id=0&t=85>
> > -------------------------------
> >
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>
> --
> Viswanadham Sridhara,
> Graduate Research Assistant,
> Old Dominion University, "VIRGINIA".
>
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