[gmx-users] FeS4 cluster

Ernesto E. Di Iorio diiorio at bc.biol.ethz.ch
Fri Dec 6 13:40:05 CET 2002

Thanks for your prompt answer, but... I could not find out what is the 
format of the file specbond.dat (I searched in the User's Guide and on the 
web). Could you please tell me what is the meaning of the various terms in 
Thanks, Ernesto
At 12:14 PM 12/6/02 +0100, you wrote:
>On Fri, 2002-12-06 at 10:58, Ernesto E. Di Iorio wrote:
> > Dear gmx users,
> > I have just installed gromacs and would like to start a simulation on a
> > protein that contains a FeS4 cluster, namely four cys residues bound to an
> > Fe atom. In the past I have simulated this protein with gromos96 and I 
> have
> > therefore all the necessary parameters to treat it. My questions are:
> > 1) Can one create a new building block for a new type of Fe, calling it 
> say
> > Fe1?
> > 2) Can one generate an own version of ffgmxnb.itp and ffgmxbon.itp?
> > 3) From what I could find out reading the User's Manual and the 
> information
> > on the web, it seems to me that most of the changes in the topology will
> > have to be done anyhow by hand, is this correct?
> > I look forward to receiving some tips from you. Should this be of help, I
> > could send you the gromos96 topology I have used in my previous 
> simulations.
>No, it's quite easy to generate the topology.
>Just add one line in the file gromacs/share/top/specbond.dat describing
>the bond between Cys and Fe.
>Then you ave to add the parameters for S-Fe to the force field files you
>listed. You can copy those files (take the ffG431a*itp files instead)
>and put them in your working directory. grompp will use those instead of
>the default ones.
>Groeten, David.
>Dr. David van der Spoel,        Biomedical center, Dept. of Biochemistry
>Husargatan 3, Box 576,          75123 Uppsala, Sweden
>phone:  46 18 471 4205          fax: 46 18 511 755
>spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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Ernesto E. Di Iorio
Institute of  Biochemistry
Swiss Federal Institute of Technology
ETH-Hoenggerberg, HPM G9.2
CH-8093 Zurich (Switzerland)
Phone: +41 1 632 3137  FAX: +41 1 632 1298

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you've not fooled yourself, it's easy not to fool other scientists. You 
just have to be honest in a conventional way after that.
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