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Revision as of 07:47, 11 July 2018
, 07:47, 11 July 2018→How to generate topology/parameter files for unknown ligand
# Go to http://ligand-expo.rcsb.org/ and use the search option to find out whether the compound is already in the PDB
# 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.
# 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]].
Within coot, you can
* use Lidia to make a chemical diagram, press "Apply" to run Acedrg
* or use Lidia to determine the SMILES string and use the "Make a Ligand" task in CCP4i2
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.
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.
