Molecular topologies for ...	... X-ray refinement/MD ...	.... drug design/docking
				Funded by:

This WWW PRODRG server will convert coordinates for small molecules in PDB format to the following topology formats: GROMOS, GROMACS, WHAT IF, REFMAC5, CNS, O, SHELX, HEX and MOL2. In addition, coordinates for hydrogen atoms are generated.

You can now also sketch your small molecule in a simple text editor, and paste this into the window below. You will be returned all of the above topology files + a GROMOS energy minimized coordinate file. Examples of this are:

    O   O          N               N           O
    |   |          |               "           "
  O=C O C=O      N=C-C-N=C       N-C-N-C-C-C-C-C-N-C-C
    | | |        |   "   |                   |   |   |
    C-C-C        C=N-C-N--                   N-C-C---C 
      |                                        "
      C=O                                      O
      | 
      O
                
  (Citrate)      (Adenine)           (cyc-Arg-Pro)

The rules:
- all atom names upper case
- use -,| for single, =," for double and # for triple bonds
- bonds running past an atom should be removed from it be at least 1 space
- no diagonal connections allowed
- bonds can be as long as you want and can contain several turns
- you can invert chirality on carbons by using a lower case c
- PRODRG currently only supports N, C, O, S, P, Cl, I, Br, F atoms
- do not include hydrogen atoms in your drawing or PDB file

This is still experimental and I would like to hear your feedback.