[gmx-users] clusters [4Fe-4S]+2

Tsjerk Wassenaar tsjerkw at gmail.com
Tue Aug 15 18:33:44 CEST 2006

Hi Elias,

pdb2gmx does not read CONECT records in the pdb file. You have to add
S(Cys) - Fe bonds in the specbond.dat file. The cause for not getting
any errors is that pdb2gmx sees cysteines, which it can handle, and
iron ions, which it can handle. But it doesn't think of connecting
them and doesn't know how to.

Besides, don't use the ffgmx force fields (browse the archives for
reasons why not).



On 8/15/06, Elias santos <silvasantosster at gmail.com> wrote:
> Hi !!
> I to construct to the block for residuo FS4 of the two clusters in the  .rtp
> file of the force field ffgmx with all the linkings, angles etc., beyond the
> on and not on parameters. When I run pdb2gmx, it does not give menssagem of
> error, but the linkings between the cysteins (SG) and atoms of iron do not
> appear in the topology  (.top) file. Although I have edited the  1jnr.pdb,
> including the conections between atoms of iron and organics atoms of the
> cisteinas.
> What it can be?
> They help me please!
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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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