[gmx-users] small molecule topologies for X-ray refinement etc.

[Daan van Aalten]

Dear structural/computational biologists

We are pleased to announce the release of PRODRG2, a web-based service for
the generation of small molecule topologies and coordinates for use with
X-ray refinement, molcular modeling, docking and simulation programs, at:

http://davapc1.bioch.dundee.ac.uk/prodrg

This version includes several significant improvements, and can now do the
following:

- take input from PDB coordinates, a "text-drawing" representation of the
  molecule, or an MDL MOLfile (generated by several chemical drawing
  programs)

- molecules can now also be drawn interactively thanks to Peter Ertl's JME
  editor

- topologies are generated for
  X-ray-related programs: CNS, REFMAC5 (new!), SHELX, O
  Docking/modelling/MD programs : Autodock 2.4/3.0 (new!), MOL2, WHAT IF,
  GROMACS

- coordinates with/without polar/apolar hydrogens are generated in PDB
  format

- add/delete hydrogens as specified by the user and (more) correctly
  detect protonation of aromatic nitrogens

- coordinates can now be minimised with GROMACS


In addition, many small "inconsistencies" (i.e. bugs) have been removed.
Calculations with a test set of 47000 compounds from the CSD show that the
GROMOS87-based PRODRG2 force field + GROMACS are able to energy minimise
these to average RMSD's of 0.04 Angstrom on bonds, 3.1 degrees on angles
and 2.0 degrees on impropers.

We would be grateful for any feedback, in particular on molecules that
"don't work".

warmest regards

Daan van Aalten & Alex Schuettelkopf

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Dr. Daan van Aalten                    Wellcome Trust CDA 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!
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     |           "     |           "      http://davapc1.bioch.dundee.ac.uk/
     C-C-O       O   C-C-C         O             programs/prodrg/prodrg.html
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