Changes

From CCP4 wiki
Jump to navigationJump to search
m
no edit summary
Line 1: Line 1: −
   
== 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.
 
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.
 +
 +
You also might want to check the NCBI Pubchem database at http://pubchem.ncbi.nlm.nih.gov/
    
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:
1,313

edits

Cookies help us deliver our services. By using our services, you agree to our use of cookies.

Navigation menu