PRODRG
From wiki.gromacs.org
PRODRG2 - will convert coordinates for small molecules in PDB format (or simply 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) of GROMOS 96.1, the original 43a1.
[edit] 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 minimisation of the ligand inside its pocket is greatly encouraged.
[edit] Resources
- MD for drug design (GROMACS) - uses PRODRG (Daan van Aalten).
- GROMACS tutorial for drug – enzyme complex solvation - used PRODRG.
[edit] References
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.
