[gmx-users] PRODRG alpha version

[Daan van Aalten]

Hi Nestor

The only think I can think of is to put something like an S or P instead
of your metal for the PRODRG input, and then replacing the
bonded/non-bonded parameters with proper ones in the resulting topology
files. As David van der Spoel suggested earlier it is important to get 
proper parameters for the metal atoms from published work. 
This approach would still save you some time.

cheers

Daan

On Mon, 28 Jan 2002 nesanfor at criba.edu.ar wrote:

> Hi;
>   Is there any alternative that generate topologies for small METALLORGANIC
> molecules? 
> 
> Thanks
> 
> Nestor
> 
> _______________________________________________________
> NESTOR EDGARDO SANCHEZ FORNILLO
> Institulo de Fisica de Liquidos y Sistemas Biologicos
> IFLYSIB
> Universidad Nacional de La Plata
> e-mail: nesanfor at criba.edu.ar
> _______________________________________________________
> 
> Quoting Daan van Aalten <dava at davapc1.bioch.dundee.ac.uk>:
> 
> > 
> > Dear GMX-ers
> > 
> > For those interested in using PRODRG to automatically generate GMX
> > topologies for small molecules, have a look at:
> > 
> > http://davapc1.bioch.dundee.ac.uk/programs/prodrg/prodrg_alpha.html
> > 
> > This version of the server:
> > - deals with molecules up to 300 atoms
> > - writes out proper GMX topologies
> > - actually minimizes your input structure with GMX using the generated
> >   topology (previously this was done with GROMOS87)
> > 
> > A few notes: 
> > 
> > - long (flexible) molecules for which you have no structure yet (so
> > using
> >   the ASCII type drawing) may be problematic as only 5000 steps of GMX
> >   steepest descent EM may not return very realistic structures. (NAG)10
> >   works fine though.
> > 
> > - please be patient when you click the "submit" button, especially if
> > you
> >   have highly branched molecules, as one of the first steps is to
> >   determine the longest path of bonds through the structures, then the
> >   next longest path on so on. Submitting a bucky-ball
> >   will cause the program to run for about 4 hours after which it
> > decides
> >   the thing is "too geometrically complicated". However, simpler things
> >   like "dodecahedrane" below work(BUT: set the "chirality" button to
> > OFF).
> > 
> >    |-----------------------------|
> >    |                             |
> >    |  |-----------------------|  |
> >    |  |                       |  |
> >    |  C-----C-----C-----C-----C  |
> >    |  |     |     |     |     |  |
> >    |--C--C--C--C--C--C--C--C--C--C
> >          |     |     |     |     |
> >          C-----C-----C-----C-----C
> >          |                       |
> >          |-----------------------|
> > 
> > - as this is an alpha version I'd really appreciate some feedback, also
> > if
> >   you succeed in getting things to work that didn't before.
> > 
> > Happy PRODRGing
> > 
> > cheers
> > 
> > Daan
> > 
> > ##############################################################################
> >  
> > 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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> > gmx-users at gromacs.org
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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