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: |