[gmx-users] FeS4 cluster

David van der Spoel spoel at xray.bmc.uu.se
Fri Dec 6 12:14:33 CET 2002

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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