Changes

== 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.

# 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.

* or use Lidia to determine the SMILES string and use the "Make a Ligand" task in CCP4i2

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]