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).
Cheers,
Tsjerk
On 8/15/06, Elias santos <[EMAIL PROTECTED]> 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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