Servers for ligand topologies/parameters: Difference between revisions

CCP4 AceDRG ([http://www.ccp4.ac.uk/dist/checkout/acedrg/doc/Manual.pdf]) needs to be fed the SMILES string of your compound, and it returns the CIF file.

Many compounds are actually already in the CCP4 dictionary. Finding out whether a compound is, is a two-step procedure:

# Go to http://ligand-expo.rcsb.org/ and use the search option to find out whether the compound is already in the PDB

# If it is, you now have a residue name. To check whether the compound is also in the CCP4 dictionary, just use the 'Get monomer' option in Coot.  

You also might want to check the [http://xray.bmc.uu.se/hicup/ HIC-Up] website, and the NCBI Pubchem database at http://pubchem.ncbi.nlm.nih.gov/. The sdf file can be downloaded and converted to PDB format.

Another solution to this problem is the [http://davapc1.bioch.dundee.ac.uk/programs/prodrg/ Dundee PRODRG server]. It is self-explanatory (you define the ligand structure by providing coordinates in PDB format, drawing molecule using [http://www.molinspiration.com/jme/ JME editor], etc.) and produces coordinates and topology/parameter descriptions in the following formats: