[gmx-users] FeS4 cluster
David van der Spoel
spoel at xray.bmc.uu.se
Fri Dec 6 15:43:50 CET 2002
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
> 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:
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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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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