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What is meant here by unknown ligand is that it is not found in the standard monomer library in CCP4 or on the [http://xray.bmc.uu.se/hicup/ HIC-Up] website.
 
What is meant here by unknown ligand is that it is not found in the standard monomer library in CCP4 or on the [http://xray.bmc.uu.se/hicup/ HIC-Up] website.
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You also might want to check the NCBI Pubchem database at http://pubchem.ncbi.nlm.nih.gov/
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You also might want to check the NCBI Pubchem database at http://pubchem.ncbi.nlm.nih.gov/. The sdf file can be downloaded and converted to PDB format.
    
There is excellent solution to this problem, and it is found on [http://davapc1.bioch.dundee.ac.uk/programs/prodrg/ Dundee PRODRG server].  It is quite 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:
 
There is excellent solution to this problem, and it is found on [http://davapc1.bioch.dundee.ac.uk/programs/prodrg/ Dundee PRODRG server].  It is quite 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:
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