Hi Elias,
Use a GROMOS96 force field (43a2, 45a3, or preferrably 53a5 or 53a6)
or OPLS, or Amber... Let it depend on the question you want to answer.
Do you want to compare with results previously obtained? Do you need
all atoms, i.e. all hydrogens, or can you do with a united atom force
field (and simulate more for the same computational cost)? Are there
parameters available for an Fe4S4 cluster for any of these force
fields? - Maybe someone has performed a simulation of a protein with
such a cluster before? Otherwise, you have to try to derive a decent
set of parameters yourself.
To build the complete topology, you have two possibilities. Either
write an .rtp entry and add the appropriate connections to the
specbond.dat file, such that you can use pdb2gmx now and in the future
for Fe4S4 cluster containing proteins, or first build the topology of
the protein part using pdb2gmx, write a topology for the FeS cluster,
add the latter to the protein topology and include the appropriate
definitions for the bonds, angles, dihedrals, pairs, etc (see Chapter
5 of the manual).
Hope this helps,
Tsjerk
On 8/16/06, Elias santos <[EMAIL PROTECTED]> wrote:
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
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:
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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
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> 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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--
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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