Hi John, In the PRODRG website, http://davapc1.bioch.dundee.ac.uk/prodrg/index.html,
Click the "Draw Molecule with JME" radio button, In the pop-up window, draw your molecule, transfer the coordinates to the server by clicking the "Transfer to PRODRG Window". You will see the coordinates of your molecule there. then "Run PRODRG" Hope this helps Raj --- On Sat, 3/7/09, Jhon Thomas <[email protected]> wrote: From: Jhon Thomas <[email protected]> Subject: [ccp4bb] refinemnet of the ligand in CNS To: [email protected] Date: Saturday, March 7, 2009, 10:48 AM HEllo all i would like to refine a ligand along with the proetin molecule in CNS. When i google about this query i get all these informations to refine the ligands in cns. The critical box to fill in is the "protein coordinate file" (your pdb filename). Then save this file to your working directory, and run it using the cns.com file which you will need to change to: #!/bin/tcsh cns_solve <generate.inp> generate.log If you have ligand in your structure you can also use generate.inp to incorporate the ligand library into the mtf file. To do this you need to generate and then save a CNS topology (.top) and a parameters (.par or .param) file using the PRODRG2 server. You then need to give CNS the pdb file for your ligand as a separate pdb file AFTER you have build it into your density, and also tell generate.inp where to find your .top and .par files. When i tried this website, it is not working or i donot know how to use. can any one suggest me how to create this dictionary file. i.e topology and parameter file for the CNS of the ligands etc. Thanks in advance Thomas
