Message: 2
Date: Tue, 15 Aug 2006 13:05:07 -0300
From: "Elias santos" <[EMAIL PROTECTED] >
Subject: [gmx-users] clusters [4Fe-4S]+2
To: gmx-users@gromacs.org
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< [EMAIL PROTECTED]>
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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" < [EMAIL PROTECTED]>
Subject: Re: [gmx-users] clusters [4Fe-4S]+2
To: "Discussion list for GROMACS users" < gmx-users@gromacs.org>
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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 < [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!
> _______________________________________________
> gmx-users mailing list gmx-users@gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to [EMAIL PROTECTED].
> Can't post? Read
> http://www.gromacs.org/mailing_lists/users.php
>
Date: Tue, 15 Aug 2006 13:05:07 -0300
From: "Elias santos" <[EMAIL PROTECTED] >
Subject: [gmx-users] clusters [4Fe-4S]+2
To: gmx-users@gromacs.org
Message-ID:
< [EMAIL PROTECTED]>
Content-Type: text/plain; charset="iso-8859-1"
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" < [EMAIL PROTECTED]>
Subject: Re: [gmx-users] clusters [4Fe-4S]+2
To: "Discussion list for GROMACS users" < gmx-users@gromacs.org>
Message-ID:
< [EMAIL PROTECTED]>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
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!
> _______________________________________________
> gmx-users mailing list gmx-users@gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to [EMAIL PROTECTED].
> Can't post? Read
> http://www.gromacs.org/mailing_lists/users.php
>
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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