[gmx-users] Program to convert GROMO96 topologies to GROMACS 3.0.x

[Claudio Soares]

On Fri, 30 Nov 2001, Daan van Aalten wrote:

> 
> Hi Claudio
> 
> Have you tried using the PRODRG server to generate topologies for your
> "strange" groups?
> http://davapc1.bioch.dundee.ac.uk/programs/prodrg/prodrg.html
> 
> cheers
> Daan

Dear Daan,

	The problem is that these are metal centres, not handled by
prodrg and not necessarely very "logical" to build. Then, the attachments
to the protein need also to be done (these are haem groups of several
types, but not Haemoglobin type haems). A topology converter would clearly
be the best. Eventually I may build one (if I can find time...), but first
I was checking if anybody had taken the time to do it.

Cheers,
Claudio



> 
> On Wed, 28 Nov 2001, [iso-8859-1] Cláudio Soares wrote:
> 
> > Dear GROMACS users and developers,
> > 
> > 	I wonder if anybody has written a program to convert GROMOS96 molecular
> > topology files into GROMACS topology files? We study redox proteins with
> > strange groups and have built programs to make patches on GROMOS96
> > topologies. Since these things are quite boring to rebuild (for GROMACS
> > topology files), I was hoping to be able to convert them and use GROMACS
> > for the simulations.
> > 
> > 	Thanks,
> > 
> > 	Claudio
> > 
> > --------------------------------------------------------------------
> > Claudio M. Soares                  |
> > ITQB                               |
> > Av. da Republica, EAN              |Phone:(351)214469610/214469100
> > Apartado 127                       | Fax :(351)214411277
> > 2781-901 Oeiras                    |email:claudio at itqb.unl.pt
> > PORTUGAL                           |http://www.itqb.unl.pt/~claudio
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> 
> 
> ##############################################################################
>  
> Dr. Daan van Aalten                    Wellcome Trust RCD Fellow 
> Wellcome Trust Biocentre, Dow Street   TEL: ++ 44 1382 344979 
> Div. of Biol.Chem. & Mol.Microbiology  FAX: ++ 44 1382 345764 
> School of Life Sciences                E-mail: dava at davapc1.bioch.dundee.ac.uk
> Univ. of Dundee, Dundee DD1 5EH, UK    WWW: http://davapc1.bioch.dundee.ac.uk 
> 
>         O     C           O     C         Visit the PRODRG server to take 
>         "     |           "     |         the stress out of your topologies!
>   N--c--C--N--C--C--N--C--C--N--C--C--O   
>      |           "     |           "      http://davapc1.bioch.dundee.ac.uk/
>      C-C-O       O   C-C-C         O             programs/prodrg/prodrg.html
>        "         
>        O         
> 
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-------------------------------------------------------------------------------
Claudio Soares                      |
ITQB                                |Phone:(351)214469610/214469100
Av. da Republica, EAN               | Fax :(351)214411277
Apartado 127                        |email:claudio at itqb.unl.pt
2781-901 Oeiras                     |
Portugal                            |WWW:http://www.itqb.unl.pt/~claudio