[gmx-users] FeS4 cluster

Ernesto E. Di Iorio diiorio at bc.biol.ethz.ch
Fri Dec 6 10:58:50 CET 2002

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 
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.
Many thanks and best regards

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

La scienza e' un sogno di infinita potenza
Science is a dream of infinite power
(Giovanni Ciccotti - Rimini, June 29, 1998)

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