[gmx-users] PRODRG alpha version

[nesanfor at criba.edu.ar]

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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