[gmx-users] FeS4 cluster

[David van der Spoel]

On Fri, 2002-12-06 at 13:40, Ernesto E. Di Iorio wrote:
> 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 
> aline?
> 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.
Here's a sample:

5
CYS     SG      1       CYS     SG      1       0.2     CYS2    CYS2

You want to add
Cys	SG	1	FE	FE	4	0.2	CYS1	FE

or something like this, if you have four cysteines bound to the FE and
0.2 nm is your bondlength.

> >
> >
> >--
> >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
> 
> The first principle is that you must not fool yourself - and you are the 
> easiest person to fool. So you have to be very careful about that. After 
> 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.
> (Richard P. Feynman)
> 
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-- 
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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