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Peng, Try the dundee prodrg server. It will let you draw a molecule or submit a .pdb and with that generate .top and .param files for CNS or the .cif file for CCP4 as well as a number of other files. The website for the server is: http://davapc1.bioch.dundee.ac.uk/programs/prodrg/ One cautionary tale recently came up (see the post from Jean on July 10th). I'll repeat my part here.
Prodrg does give weird atom names...And if they conflict with heavy atoms, then as you've found it can cause problems. The general workaround that I have used is to draw the ligand, and submit that to prodrg. Then take the output .pdb file and change the names of the atoms and re-run prodrg with this .pdb. This gets rid of 99% of the problems, but manual editing of the parameter and topology files is still sometimes necessary.
Best Wishes, -bob On 7/12/06, Peng Xie <[EMAIL PROTECTED]> wrote:
Dear all, I am trying to do my refinement together with my ligand using CNS. I used the HIC-up server to generate .top and .par files using the .pdb of my ligand. Surprisingly, the server returned those two files with a lot of the statements missing from the parameter files (such as nonbonded, IMPRoper, DIHEdral parameters). I managed to add nonbonded parameters manually but I don't know how I can add the rest of the statements into the file. I am wondering if there is anybody who had this problem before or is there anything that I did wrong along the way. Any advice will be really appreciated. Thank you very much! Best, Peng
