[gmx-users] PRODRG alpha version

[Daan van Aalten]

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