[ccp4bb]: small molecule topologies with PRODRG

[Daan van Aalten <dava@davapc1.bioch.dundee.ac.uk>]

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Dear CCP4-ers

Tired of making those small molecule topologies by hand, or perhaps don't
even have a PDB file to start with?
Please visit 
http://davapc1.bioch.dundee.ac.uk/programs/prodrg/prodrg.html

This will do several things:

- generate a topology + parameters for CNS/SHELX (and many other programs)
  starting from PDB coordinates *OR* an ASCII drawing of your molecule.

- return you with a GROMOS energy-minimized coordinate file + O torsion
  data base so you can easily map-fit your molecule as well.

- many other things, see web site.

This program differs from the excellent Hic-Up service from Gerard
Kleywegt in that it actually determines bonding parameters from the PDB
file (and it'll warn you if your PDB file contains strange geometry)
rather than restraining bonds to the values determined from the
coordinates. In addition, the new text-drawing input may prove useful.
Current large scale runs on the CSD indicate that the structures refine
close to the experimental structure in most cases.

This is an alpha version and I would really appreciate any feedback you
may have.

Cheers

Daan


##############################################################################
 
Dr. Daan van Aalten                    TEL: ++ 44 1382 344979 
Wellcome Trust Biocentre, Dow Street   FAX: ++ 44 1382 345764 
Div. of Biol.Chem. & Mol.Microbiology  E-mail: dava@davapc1.bioch.dundee.ac.uk 
School of Life Sciences                WWW: http://davapc1.bioch.dundee.ac.uk
University of Dundee, Dundee DD1 5EH    
Scotland, UK.