[gmx-users] FeS4 cluster

[David van der Spoel]

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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