Servers for ligand topologies/parameters: Difference between revisions

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== How to generate topology/parameter files for unknown ligand ==
== How to generate topology/parameter files for unknown ligand ==


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.
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 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.


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:
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]  
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