[gmx-users] Fe - Cys S bonds

Tsjerk Wassenaar tsjerkw at gmail.com
Sat Jul 29 22:13:44 CEST 2006

Hi Elias,

Unless you're doing QMMM calculations, it is out of the question that
bonds are broken and formed during your simulation. Whether atoms are
bonded depends merely on the definitions in the topology file. The
bonds you see in a structure visualization program are usually
inferred from distances and therefore you can conclude that some atoms
which are bonded get away from each other, despite the bonds, while
atoms which are not bonded appear to give strong interactions,
bringing them at too short distances (displaying as bonds).

To cut it short, you have a problem in your topology. Also, an iron
cluster will be problematic in terms of the parameters. Where did you
get your parameters or how did you derive them?


On 7/29/06, eramos at cefetba.br <eramos at cefetba.br> wrote:
> Hi all,
> I am simulating a metalloprotein with two 4Fe-4S cluster. In the pdb file
> Fe atoms are covalently bonded to Cys-S atoms. However, after minimization
> the Fe – Cys S bonds atoms are broken and new bonds Fe-Fe inside the
> cluster are formed. Is it possible to impose that bonds Fe – Cys S atoms
> are not broken both in energy minimization and in md run?
> Thank you in advance,
> Elias Ramos de Souza
> Grupo de Pesquisa em Biofísica Teórica e Computacional
> Departamento de Ciências Aplicadas
> Centro Federal de Educação Tecnológica da Bahia
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Tsjerk A. Wassenaar, M.Sc.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336

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