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Servers for ligand topologies/parameters: Difference between revisions
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→How to generate topology/parameter files for unknown ligand
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== How to generate topology/parameter files for unknown ligand == | == How to generate topology/parameter files for unknown ligand == | ||
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]]. | |||
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. | |||
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: | |||
- [http://www.rcsb.org/ PDB] | - [http://www.rcsb.org/ PDB] | ||