[gmx-users] edit specbond.dat file

[Elias santos]

Message: 2
Date: Tue, 15 Aug 2006 13:05:07 -0300
From: "Elias santos" <silvasantosster at gmail.com>
Subject: [gmx-users] clusters [4Fe-4S]+2
To: gmx-users at gromacs.org
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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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Message: 3
Date: Tue, 15 Aug 2006 18:33:44 +0200
From: "Tsjerk Wassenaar" <tsjerkw at gmail.com>
Subject: Re: [gmx-users] clusters [4Fe-4S]+2
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
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       <8ff898150608150933l103408e5k41bf57b0c8535817 at mail.gmail.com>
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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 <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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Hi!!
 Which the force field can be used in this situation?
As I fill the fields of the archive specbond.dat for linkings between atoms
of Fe of residue FS4 and SG of residuo of cysteins.?
Elias
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