Gromacs

PRODRG

    Table of contents
    1. 1. Tips
    2. 2. Resources
    3. 3. References

    PRODRG2 - will convert coordinates for small molecules in PDB format (or simple text structures) to the following topology formats: GROMOS, GROMACS, WHAT IF, REFMAC5, CNS, O, SHELX, HEX and MOL2. In addition, coordinates for hydrogen atoms are generated.

    There are actually two versions of the program:

    • PRODRG 2.4 : produces coordinates and topologies for the ffgmx force field, which is now deprecated in GROMACS.
    • PRODRG 2.5 beta : you can select the force field ffgmx (deprecated) or GROMOS 96.1, the original 43a1.

     

    Tips

    If you're including a molecule from an already existing conformation (typical case: crystallography, NMR structure), you may wish to avoid the minimization of the output structure in order to keep your original coordinates intact. Please be aware you'll need to take a further look at specific bad contacts that may arise when using this approach. An energy minimization of the ligand inside its pocket is greatly encouraged.

    The charges and charge groups generated by PRODRG are typically not consistent with functional groups that were derived more rigorously for the force field of interest. It is therefore the task of the user to validate any parameters obtained, and to modify them, if necessary, since the artifacts of not doing so are now published.  A thorough understanding of the underlying force field theory is recommended.  See the parameterization page for more details.

     

    Resources

     

    References

    1. A. W. Schuettelkopf and D. M. F. van Aalten. (2004) PRODRG - a tool for high-throughput crystallography of protein-ligand complexes. Acta Crystallographica D60: 1355-1363.
    2. D. M. F. van Aalten, R. Bywater, J. B. C. Findlay, M. Hendlich, R. W. W. Hooft, and G. Vriend. (1996) PRODRG, a program for generating molecular topologies and unique molecular descriptors from coordinates of small molecules. J. Comput.-Aided Mol. Des. 10: 255-262.
    Page last modified 17:59, 30 Nov 2010 by JLemkul?